I've done a search and found similar issues, but none that address the issues I'm having.
I am having a problem with a Core 2 Duo MacBook running 10.4.11. I'm not the primary user of the computer, so I don't have much information on what the user was doing when the problem first started happening (he was surfing MLB.com, he hit return after entering something in a search field and Safari crashed. After that, everything was broken).
The dock icon reverted back to the default set, Safari's default settings revert back to the default settings. FileVault is enabled, and I wonder if that has something to do with the difficulties. Finally, the GarageBand application is missing, but not the prefferences and supporting files. I suspect that missing application is something different altogether, but it wasn't discovered until all this weirdness began.