OS X fonts have been a particularly annoying problem. Some applications, like my 5 yo copy of FileMaker Pro 8, show persistently garbled fonts. On the other hand, my new copy of Numbers.app defaults to a poorly rendered 9 point Helvetica Neue.
I've lived with these bugs for years, but tonight, in the process of investigating a hung app, I sorted them out.
In Library/Fonts (see Mac OS X: Font Locations and Their Purposes) I found a folder of Microsoft Fonts left over when I deleted Office 2008, and I found a good number of old style fonts dating back to 2006 . After cross checking with the excellent font lists in the extensive article Font Management in OS X I removed those fonts. This had the unexpected benefit of fixing FileMaker Pro 8 - the fonts there now display nicely.
For the Numbers font problem I experimented with control of OS X antialiasing. In OS X Preferences:Appearance I set "turn off text smoothing for font sizes" to 8 and smaller (it was initially 10 and smaller).  I'm not sure that made any difference. What did help was creating a new template with all cells set to Helvetica 12, then saving that as a template and making it the default spreadsheet to use on startup. (Currently there's no other way to change the default font in Numbers.app.)
In the course of the above I found:
- When I opened up Font Book.app several of my fonts showed a duplicate font message. When I ran verify some reported bugs. I chose the inactivate duplicates option, but I later discovered OS had inactivated the "good" version of the font. After I removed my old fonts I had to re-activate the "duplicates".
- The Font Book app can be used to verify all fonts. I recommend that quick test for everyone who's run OS X for a while.
- It's convenient to use Font Book to create a collection of the handful of fonts I actually use. Note the Windows Office Compatible and "Web-safe" built-in collections.
- My copy of OS X includes two SchoolHouse fonts - cursive and printed. I wish I'd had these when I was teaching writing to my first child! I don't know where they came from, I don't think they're part of the regular OS X font installation.
 The options in 10.6.7 are different from the options in 10.6 in Aug 2009.
 The accounts on my 27" iMac have migrated across many machines, probably going back to 10.1. They've picked up some cruft along the way.
Update 5/28/11: I should have tested FileMaker Pro 8 a bit more. It looked good at first, but when I searched later all my records seemed blank! A reinstall, surprisingly, didn't fix anything and didn't seem to add new fonts. I had switched to Verdana, and tried old Georgia instead. That worked well.
Update 5/30/11: When I tried to empty the trash I learned that Arial and Times were still in use! They were in the Microsoft Fonts folder, and they were my bad-boy fonts. I had to restart then empty the trash.