Update: While the tip below refers to Firefox 2 and 3, at least some of it applies to newer versions of the Firefox web browser as well which means that it can still be useful to you.
I finally upgraded from Firefox 2 to the latest release candidate of Firefox 3 and immediately ran into a problem. My RSS feeds were not showing up at all in the Bookmarks anymore.
I was able to get them back after importing an old bookmarks.html file from the Firefox profile folder into the browser but it had the consequence that every bookmark was available twice now.
Took a while to remove the duplicates again but I now have my RSS Feeds in the Bookmarks Folder as well.
It turned out that my favorite RSS add-on Brief for Firefox was not compatible with the release candidate 2. I tried to force compatibility which did not work either.
Now here is the interesting information that might help you if you ran into a similar problem. If one of your add-ons is not compatible to the latest Firefox version you can look for a development version instead.
The two locations where you find development versions posted are on the developer website or on the Mozilla AMO page of the add-on. If you select the later, expand the Version Information module on that page and click on "see complete version history" afterwards.
There you may find listed newer versions that have not been fully reviewed by Mozilla yet or have been added by the author as development versions that are not released to the main channel.
It turned out that the developer was busy creating Brief beta versions, the latest on his homepage was Brief 1.2 beta 2 while the latest on the official Mozilla website was Brief 1.1. Brief 1.2 beta 2 is fully compatible to Firefox 3 and I was able to select my feeds and use the RSS Feed add-on ever since.
To sum it up. If you have an add-on that you need but that is not compatible try to force compatibility.
If that is not working check the developers homepage and Mozilla's Add-on repository for new versions.