Mac OS X: About the Archive and Install feature
This goes into detail for you. It's a quick and dirty way of getting system files back in line.
If the OS is still slow after that, backup and do Erase and Install, which wipes all.
So it seems Snow Leopard does that automatically. I'm nervous to wipe everything and reinstall. Seems like a huge pain for something that I'm not sure will fix my problem.
My stupid machine takes 5+ minutes to boot, and things are getting worse.