When I updated to 3.4.2-13 (x86_64), no plugins were loaded. This affected plugins which I installed using the Eclipse update UI as a user (pydev) as well as plugins installed through Fedora's rpms (eclipse-emf-2.4.2-3.fc11.noarch for example). I was not able to re-install these packages because Eclipse's update manager found that the plugins were already installed. eclipse -clean did not help eclipse -console showed that the plugins were not loaded. There are no errors in the log. By removing all my configurations (rm -rf ~/.eclipse) I could see all the plugins again on a new workspace but re-installing everything is not an option. I downgraded to 3.4.2-11 and everything works again.
This is an upstream bug in the 3.4 series. It's fixed in 3.5 which will be in Fedora 12. *** This bug has been marked as a duplicate of bug 509616 ***