If you open FontBook and see dots at the end of the font name, it means you have duplicate copies of that font installed in your system. To get rid of these, select the version of the font you want to use, and then click Edit -> Resolve Duplicates. This turns off the other copies.
A seen here, holding your mouse pointer over each font and leaving it there will display type, version, and path information to help you determine which font to disable.
[robg adds: While FontBook won't replace pro-level tools (which is a good thing, in my mind), it's a nice solution for casual font users such as myself. If you haven't checked it out yet, it's worth a look.]

