For weeks I have had Font issues. I must have either made some mistake or chosen the wrong option with Font Book, but a number of apps that relied on specific system fonts were beginning to regularly crash, or display awkwardly in a different font. This is a technical hint, but I used this to get back to normal. This may also work with earlier versions of OS X, but I know it works with Tiger.
To prepare, enable Remote Logins via ssh (in the Sharing System Preferences panel) just in case. Make sure you can login from remote before proceeding!
[robg adds: This hint is quite dangerous, as it involves removing system fonts from a live machine. Proceed at your own risk, and probably only after exhausting other methods...]
First, (as root) run:
$ sudo rm -rf /Library/Fonts/*
Yes, quite extreme. At this point, you either get lucky and Terminal continues to run, or it crashes on you. If it crashes, I hope you made sure you can get in via ssh. If not, you'll be booting single-user, and mounting the root filesystem read/write just to continue.
$ rsync -av --delete /System/Library/Fonts/ /Library/Fonts/
Important: Ensure you have the trailing / on each path, as this tells rsync to sync the contents of one directory to another. At this point, Terminal may again crash. If you've made it this far, you can probably re-open Terminal and it will find its fonts. If not, use ssh.
$ cd /Library/Fonts
$ ls -l | grep ' 0 '
This should give you a list. Remove each with
$ rm font_filename
You will need to use 'or " around the filenames if there are spaces in the filenames. Now, open Font Book. One by one, go through the "Computer" fonts group, selecting each font that has a dot next to it. Use Edit: Resolve Duplicates. Quit Font Book.
$ cd /Volumes/Mac\ OS\ X\ Install
$ find . -name AdditionalFonts.pkg
$ open /path/to/AdditionalFonts.pkg
Install the additional fonts to the system.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060323201534331