When the Shit Hits the Fan (Part 1 - OSX and Maintenance)
Here's a guide of the steps to take when disaster strikes. Much of what follows is general advice to do with keeping your Macintosh computer running smoothly (and what to do when it doesn't), as this relates to a Mac used as a Digital Audio Workstation (DAW).
Then, in Part 2, there are some suggestions about solving Logic Pro (my DAW of choice) startup and crashing problems.
Backup and Routine Maintenance
Of course, prevention is vital. Sooner or later, you'll run into trouble but if you have taken some preventative steps, and you have backups, a potential disaster becomes no more than a minor annoyance.
You need three backups.
1. At least two backups of your vital data, one offsite and one conveniently available which can be quickly restored. OS 10.5 (Leopard) introduced Time Machine. Use it! It's a good first step, and allows you to quickly restore files. Use an external drive for this, and USB is fine. It doesn't need to be fast, as once your initial backup is complete, hourly backups shouldn't take very long. Don't use an internal drive for Time Machine backups - if your computer dies because of a hardware problem, you don't want to extract hard disks and put them into another machine, or install them in a firewire HD enclosure.
For offsite backups, check into Carbonite, Mozy, or IDrive. If you have a .mac or mobile .me account, that can be used too, or even the great DropBox. All of these cost money, but one day you'll be glad you made the investment. You need offsite backups in case of fire, theft, flood, angry partners (business or domestic) or an incontinent pet. For offsite backups, don't bother to backup applications or the system: you already have those (hopefully) on the original media. Just concentrate on your data, including anything you have on secondary drives (Logic projects, for example). Similarly, don't backup samples, unless you created them. 3rd. party stuff is already on the CD/DVDs they came on, and any updates to these libraries can be re-downloaded on line.
2. A clone of your essential system and applications. Ideally, this should contain your latest, solid, system with your essential applications. In my case, I created a clone with SuperDuper and use their sandbox system for day-to-day work, while keeping a pristine 'safety' system on another hard drive or partition, which shares data with the original. This means that I can try out upgrades and new software. As I also beta test software; this method means that I can play around with iffy versions of software without putting my main system in jeopardy. If you have any flavor of a Mac tower computer, use one of the internal bays for your clone drive. If you use a Macbook or an iMac, use an external firewire drive. Using partitions, you could use this drive for storing samples too, although I prefer not to use this drive for anything other than the safety clone.
3. Also use external firewire drives to backup everything. You could use a SuperDuper script to run scheduled incremental backups once per day, when you're not working. This drive should be turned off, except when backing up. Finally, Drobo is a great solution if you have the budget.
Hard Disks
When you buy an external hard drive, the chances are that out of the box it won't be formatted properly to work with a Mac - it' will probably be formatted as FAT32. So before using it for real, plug it in, and run Disk Utility. Format and name the drive, choosing Macintosh OSX Extended. If it will be a system boot drive use the GUID partition map if you're using an Intel Mac. I'd suggest that journaling be off for a data drive (audio projects, samples etc) but on if it's a system volume.
Common Problems
Here's a couple of typical cries for help:
"There was a power outage but on rebooting I had somehow corrupted my drive so now when I plug it in all it says is this disk cannot be read"
Usually, when this happens, the hard drive is physically fine - what has happened is that the disk directory has become scrambled so that the OS can't find anything, including the directory itself. Disk Warrior is the tool of choice for these problems and every Mac user should own it, in my opinion. If Disk Warrior can recognize the disk, it will usually be able to construct new directories and your disk (and your data) will be fine.
"My hard drive is making an odd clicking sound"
It's in its death throes. Back it up immediately, and replace it. After it's backed up, you can reformat it, and maybe use it for some non-essential storage in another computer but usually clicking or thumping noises mean that it's about to die. Same advice if it takes a lot time to appear on the desktop, accompanied by a grinding noise.
Using a UPS (Uninterruptible Power Supply) is also a worthwhile addition to your setup. Plug your computer, and any external hardware into a UPS and you'll have some time to shut down gracefully in the event of a power outage and as a bonus usually some power conditioning. APC and Tripplite are good manufacturers of UPS systems.
Partitions
Partitioning is useful for housekeeping purposes, but worthless if you think that somehow making multiple partitions will speed up performance. HD platters are connected - if your system is looking for stuff on partition A at the same time as streaming audio files from partition B, performance will suffer. This is also why recording to your system drive is a Bad Idea - as the OS is trying to access application data and resources, the application is also trying to retrieve audio data at the same time. Keep your projects on one separate physical drive, and everything else (system and applications) on another drive. For those who use huge sample libraries, a third drive is a good idea - you can also use the sample drive for Logic's Apple loops if you use them.
Hard drives are cheap. As I write this (Jan 2010) a Seagate Barracuda 7200 rpm 1TB or 1.5 TB drives are around $100 and are perfect for backup drives and sample drives, and even audio project drives unless you record a lot of audio/playback, in which case a 10,000 rpm drive can give greater performance. I use Western Digital's 300 GB Velociraptors for audio drives.
Although they are much more reliable than they once were, hard disks will go bad - it's not a case of if, it is a case of when. Remember this, and plan accordingly.
Bad Memory
This too ranks up there with disk permissions, defragmenting and all the other near myths. I tried to count how many Macs I've owned (I got to about 30 and gave up) and I have never had a bad memory stick. I have cracked a edge connector, and I dropped one once and stepped on it, but I haven't had one that has gone bad. I'm not saying it can't happen - I'm saying it's rare. If your Mac is crashing, suspect bad software, a corrupted or damged drive or bad hardware in that order. As the old saying goes, "if you hear the sound of hooves thundering down the road, first suspect horses, not zebras." If you really think you might have bad RAM, use the hardware test disk that (probably) came with your Mac, or download Rember (memtest GUI)
System Maintenance
With later versions of OSX there really isn't much you need to do. However (perhaps because of a mild case of OCD) there are still some preventative steps I routinely take.
Alsoft's Disk Warrior. Buy it. It's one utility that will get you out of trouble more than anything else I've found. When you buy it, install it on every bootable drive you own, as it runs slowly from its CD. Many apparent hard disk problems are really disk directory glitches where files seem to be damaged, missing or corrupted. Disk Warrior creates an optimized disk directory, fixes many different types of file/directory problems and your disk runs noticeably faster. I run this once per month.
OSX Disk Utility is handy too. If you notice a problem, run it immediately, using 'verify disk' if you don't have Disk Warrior.
Permissions
There's a bunch of folklore surrounding permissions. Reading online forums, you'd think that incorrect permissions account for 99% of problems, including spontaneous combustion of power supplies, logic board failures and world hunger.
In fact, damaging permission problems are quite rare, unless you regularly access other people's hard disks or data files/folders which you use for working on projects. Problems can occur when installing new software, so if after installing something new you notice that something changed, it's worth running a permissions check. Apple's Disk Utility will do this for free. There are lots of utilities which will correct permission settings, such as Cocktail or Onyx (be careful with Onyx, and read the instructions). I prefer to use Atomic Bird's Macaroni which runs in the background and handles OSX maintenance scripts automatically on its own schedule. If you use multiple user accounts, be sure that any installations are always performed when in the account you will be logged in with for using of the software.
For those cases when you want to force permissions to allow yourself access when OSX thinks you shouldn't have them, BatChmod is invaluable, but please read the instructions first, and don't use it at all if you're unsure about what you're doing.
If all of the foregoing seems a little daunting, remember that it only takes a few hours to set up: going forward, it's all mostly automatic. Try it, and sleep well at night.
System and Software Updates
As soon as Logic 9 or Snow Leopard became available, the support forums were full of messages complaining about bugs, unexpected behavior, hardware not working, plug-ins not loading etc. What do these people expect? Never use the X.0 version of anything, unless you've followed my earlier advice about using a sandbox. In that case, it doesn't matter as you can easily revert to your existing virgin system.
Unless there's a compelling reason to upgrade, wait a few weeks and let the early adopters report back and then make your decision. I know it's hard to resist: when Logic 9 was released, it included many features that Logic users have begged for. But unsurprisingly, many of these features didn't fully work until the release of 9.0.2 and even now some features are still problematic. Snow Leopard has nothing that I need, so I don't use it (yet). In fairness, it was never intended as a feature release; it was more an optimization release, but unfortunately broke some apps and introduced some hardware compatibility. I bought Logic 9 (or Studio 2, whatever it's called) and Snow Leopard and tried it out (but on a separate drive). Some new features are very nice, others need updates. I continue to use 8.0.2 in 10.5.X which is quite solid. Eventually I'll jump over, but not yet, particularly when I found that the RAM footprint of LP 9 was at least 500MB higher that LP 8 and some of my 'heavier' current projects wouldn't run in 9.
Summarizing, don't jump on to the new versions of anything until you're sure that (a) you need it, (b) you have backups to revert to, and (c) your essential hardware and software will work with the new software and (d) you've upgraded all necessary drivers and versions to support the new major upgrades, and found out before if updates are even available.
Finally, don't install different updates at the same time. Ever.
Update OSX first. Test thoroughly. If all is well, then install major application updates. Test thoroughly. Install add-ons, one by one, testing between each one. If you install them all at once, you'll have trouble figuring out which new install caused a problem, should one surface.
Reinstallation of System Software
Theoretically, this shouldn't be necessary. However, 'shouldn't' isn't as good as 'never.' Every time some software freezes, hangs, unexpectedly quits or just plain crashes or you have to use 'force quit' there's a chance that somewhere in the depths of OSX's system files, a bit got flipped, an entry in a shared library got changed or some other tiny fragment of a file became corrupted. Over time, these minor errors add up, and in turn affect other files, which causes other corruption, and so on. The domino effect.
The solution: periodically run an 'archive and install' from your system disks, and run all the updates. It takes a few hours, but typically I do this every six months, or if I notice any instability (quite rare). Once you've done it a couple of times, it's very easy, and is a great opportunity to dump stuff you've acquired over time that you really never use. It's quite surprising how smoothly everything runs afterwards.
Start Up Issues
If your Mac won't boot, or you get kernel panics or other problems, restart holding down the option key after the chimes. From there you can choose another start up disk. Obviously turn on any bootable external drives, and attach a wired keyboard - wireless keyboards and mice won't help you as the software required to initiate wireless access loads later than the disk selection 'option' command needs.
All the OSX keyboard short cuts are here (with links to further explanation), but the following are the most useful when you have a problem:
C : Forces most Macs to boot from the CD-Rom drive
T : Target Disk Mode (FireWire) – Puts machines with built-in FireWire into target Disk mode
Mouse Button Held Down : Ejects any mounted removable media.
Shift : Boots into safe mode. This can take a while. Safe Boot forces a directory check of the hard drive. This is identical to using Disk Utility's Repair Disk or the fsck -fy terminal command.
Command-V : Boots Mac OS X into "Verbose Mode", reporting every console message generated during startup. This shows what’s going on behind the scenes with your machine on startup, and can be very useful.
Command-S : Boots Mac OS X into "Single User Mode" – helpful to fix problems with Mac OS X
Command-Option-P-R : Erases PRAM if held down immediately after startup tone. You will hear a chime when this has erased the PRAM; often it's suggested that you hold this key combination for 3 chimes to completely flush the PRAM. (rarely needed, check first)
Command-Option-O-F : Boots the machine into Open Firmware
Command-Option-Shift-Delete : Forces your Mac to startup from its internal CD-ROM drive or an external hard drive.
Disk Fragmentation
I don't defragment drives, mostly because I keep my drives with usually 30% minimum free space and OSX does a good job with keeping files under 20MB defragmented, which easily covers 95% of the files on my system drive. On my audio drives, I keep projects on them only until they're completed, and then I archive them. So the only projects on my audio drive are those with which I'm currently working. Copying files from one disk to another defrags. them anyway, so I don't concern myself with defragging drives. Also there's one important reason not to - if you use Logic 9.0.2 or earlier, and use long file names, Logic will truncate them and include numbers referring to the position of that file on the disk. If you defragment your drive, Logic can 'lose' you files, and you'll have to manually find them within the Logic project. Time-consuming, annoying and definitely not fun.
Your file names should be kept at under 32 characters including the file extension. So if your audio file is named "Mysongname-gtrsolo-verse3-take4.wav" it will be truncated by Logic to something like "Mysongname#A27596.wav" If that file is then moved (by defragmenting, for example) you're screwed. 
The next time you open that project, you may get an unpleasant dialog saying: "Mysongname-gtrsolo-verse3-take4.wav" cannot be found - options: search or skip.
Be careful!
More Help:
Resolve startup issues and perform disk maintenance with Disk Utility and fsck. A very useful article for when you don't have an alternative disk to boot from (and you have unwisely ignored all the above advice).
Guest Account
Always set up a guest account on your Mac. In case of problems, log in to this guest account first and see if the problem persists. If it's gone, you have some corrupted files in your main user account; probably preferences in the Library/Preferences. So if you have a problem with Logic launching, for example, this is the first step. Don't use this account to install updates or new software.
Keep an Old Machine
Having a second Mac is useful. When you buy a new machine sometimes it's tempting to sell or give away your old machine. Try to keep one - even an older Mac is a perfectly capable machine for internet use, running a browser and downloading updates of software. Even simple stuff like archiving and installing can be sped up while your main computer is having major restoration; you can be downloading updates, for example, or reading online support documentation.
Next: When the Shit Hits the Fan (Part 2 - Logic Pro)