For example, the document I was editing used Times New Roman, but featured a bunch of Unicode-based greek letters to connote certain medical thingamajigs. However, the thingamajigs kept displaying as boxes -- i.e. no such character existed. It turned out the the version of Times New Roman that I was using was outdated, even though I had a newer version already installed.
MS Office 2004 installed the newer version of the font in my user's ~/Library/Fonts folder. The one installed by Apple with the OS was installed in the top-level Library/Fonts folder. When you open Font Book with two versions of the same font, they naturally register a conflict, but because the older version of the font is in the root /Library/Fonts/ folder, it takes precedence over the newer version in the user-level Library/Fonts folder when you elect to 'Resolve Duplicates.'
That means that if you're not paying attention, you'll probably disable the version of the font that gives you Unicode support. In my case, the version in my user's Fonts folder was version 3.05, and the one in the root Library folder was 2.60. When I blithely Resolved Duplicates, Font Book disabled the newer version due to its secondary location.
Once I disabled the old version and enabled the newer version, the missing Unicode characters properly displayed within my document (before and after shot). For what it's worth, the earliest version of Times New Roman that supports unicode seems to be 2.76.

