Generally speaking, it's not a bad idea to open Applications > Utilities > Disk Utility and run repair permissions.
Briefly, permissions control who/what has access to the various files, folders and applications on your system. Permissions are something that are a function of the UNIX underpinnings of Mac OS X and are quite responsible for the much improved security of Mac OS X over the "other" product.
To make sure that file system damage is kept in check, you might consider purchasing a copy of DiskWarrior from Alsoft. Note that you CANNOT repair a file system while booted from it, that's why you need the DiskWarrior disk. Mac IT pros like me boot customers' computers from another drive to isolate hardware issues from software issues and run disk diagnostics on hard drives. DiskWarrior comes on a bootable disk so that you can boot from it to check and repair your internal hard drive.
Be aware that if you purchase any kind of tool that works to fix issues either with the OS or the file system you want to MAKE CERTAIN that what you're running is compatible with the version of OS X that you're running. DO NOT assume that if you get a DiskWarrior disk today that it will be compatible if/when you upgrade to the next version of Mac OS X. The same is true for OnyX, TechTool Pro, Cocktail, or anything else designed to improve or repair your system.
That said, the best method to avoid disaster is to have a backup. If you have Leopard, and I'm assuming you do, take advantage of Time Machine by getting an external hard drive (or a Time Capsule) and dedicate it for use with the Time Machine software included in Leopard.
One of the absolute best resources for troubleshooting a problem is the various Mac-related forums on the Internet including this one, Apple's Discussion lists
http://discussions.apple.com/ and various others. If things ever get real nasty, you're probably going to want to seek out professional help to ensure that your precious data is cared for properly -- especially if you're silly enough to operate without a good backup.
Another thing to keep in mind is that the more stuff you install, the more potential you have to slow things down. You're not really slowing down the computer itself, rather you're giving it more to do. For example, there are plenty of little gadgets and utilities out there that might sound fun or useful on the surface so you install them, use them for a bit and then forget about them. Many of these little utilities will install software that starts up when you boot up your computer or when you log in. So they'll be running in the background chewing up RAM and processing resources. Keeping it clean is the BEST way to operate. Don't install stuff that you're probably not going to use. And ALWAYS make sure what you DO install is compatible with the version of Mac OS X that you're running on your computer.
Hope that's all helpful!