Sometimes, just sometimes you jump the gun and upgrade too soon. Well as it turns out I did that when I first started my new job. Our home grown web app renders perfectly in Firefox 2 but looks odd in Firefox 3. Also one of the plugins we need to run is very unstable in Firefox 3 so I had to revert back.
If I had known this a month ago and not started accumulating bookmarks all over the place I would have been fine, but that was not the case. The main problem is that Firefox 3 uses a new places.sqlite SQL database to keep track of bookmarks instead of the tried and true bookmarks.html. I went online looking for some sort of conversion program, thought about making my own (which I still might do just as a proof of concept / fun project.)
So anyway, here is how to have Firefox 3 save a bookmarks.html file in addition to the places.sqlite. Open a new tab and go to about:config. Click "Ok" when it asks if you will be careful. Now browse down to "browser.bookmarks.autoExportHTML" and change this from the default of "false" to "true". Restart Firefox and you will have your bookmarks.html file updated as you add new bookmarks.
If I ever do create a conversion program I will post the link on this site.