It happened also on older versions but it does happen more frequently on the “final” 2.1 version. FYI : Gentoo Linux, Eclipse gtk, seems to be related somehow with bug 33138 (don't have the time to dig further).
Sometimes the monster simply hangs during a [take your pick : refactoring, new class generation] with an empty progress bar in the dialog box and a completely useless “Cancel” button. Been there, done that : kill -9 …
Then, trying to re-start Eclipse leads to a deadlock – while recovering workspace : dialog box, empty progress bar and useless “Cancel”. Freezed !
I have a lot of settings and projects so deleting the whole .metadata directory is just too painful. Therefore, I had to find out a smaller workaround : just delete the file .metadata/.plugins/org.eclipse.ui.workbench/workbench.xml and Eclipse restarts with a clean workspace. Some adjustments are lost but hey – my metadata is still there.