Bookmarks are stored in a separate folder, in your Firefox profile, which is usually located in C:\Documents and Settings\[Username]\Application Data\Mozilla\Firefox\Profiles\xxxxxxxxxx. Unless you have deleted this profile folder, your bookmarks should still be there. My guess is that you may have switched profiles, and perhaps the bookmarks aren't loaded in the profile you are using? If that is the case, just copy them across from one profile folder to the other, or switch back to your original profile. Reinstalling Firefox won't have any effect, if the bookmarks.htm isn't in the profile folder you are using.
Lona's link, by the way, looks very useful.