There have been many hints concerning Extensis Suitcase bugs and general font management issues. However, I can find no link to a very helpful PDF from Apple called Using and Managing Fonts in OS X that contains key information about how OS X deals with fonts, where it puts them, and which fonts actually need to be installed for everything to function properly.
The PDF is chock full of marketing babblespeak, but is still helpful, especially the sections that address creative professionals whose font libraries may conflict with pre-installed system fonts. Note the screenshot (at the bottom of page 10) that shows the small number of Classic fonts that are really needed by system resources -- the document also advocates removing the dreaded Helvetica and Zapf Dingbats .dfonts!
As usual, tamper at your own risk, but I've found that establishing a minimal system font base greatly facilities setting up and maintaining Suitcase X1.
[robg adds: It took a bit of digging to find this link -- the one submitted with the story no longer worked. A few searches later, and I found that Apple had recently moved it from the "top level" of their site into an archive folder. As such, if you want the PDF, I'd suggest grabbing it quickly; I'm not sure what the lifespan of the archive folder might be...]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040123134139224