Shawn Blanc recommends:
use SuperDuper to keep a bootable copy of your main startup drive, and let Time Machine do its thing to archive stuff
When Time Machine was announced, I’ve scratched my head for a while, clueless as to why people were finding it useable at all. One day the realisation finally hit me: I had failed to distinguish between archiving and backing up. To me, this is the same thing, because when I want to make a backup copy of something, I copy it to my archive, which is a somewhat robust data store, with the most important bits copied ‘off site’. Of course I do this way too infrequently, and I still haven’t made a properly searchable index, but when some ancient file is important enough to me to go through the effort, I can find it and get it back. Time Machine doesn’t allow you to do this. A few examples for things you might expect from a proper archiving solution, where Time Machine fails: It haemorrhages old data, it doesn’t allow you to sort your data onto multiple volumes in an intelligent way, it can’t deal with small changes in large files (not in a sensible manner that is).
Time Machine does not archive stuff.
All it does is make backups, frequently, all the damn time, which is something you’ll never do yourself. That’s why you should use it. Using SuperDuper in addition is also a good tip, as Time Machine can’t make bootable backups.