This happens to me all the time.
Go to the error log, find the exception, and open a few levels until you can see something more like a root cause. Does it says "Resource is out of sync with the file system" ?
When renaming packages, of course, Eclipse has to move files around in the file system. Apparently what happens is that it later discovers that something it thinks it needs to clean up has been renamed, can't find it, throws an exception.
There are a couple of things you might try. First, go to Window: Preferences, Workspace, and enable "Refresh Automatically". In theory this should fix the problem, but for me, it didn't.
Second, if you are doing a large refactoring with subpackages, do the subpackages one at a time, from the bottom up, and explicitly refresh with the file system after each subpackage is renamed.
Third, just ignore the error: when the error dialog comes up, click Abort to preserve the partial change, instead of rolling it back. Try it again, and again, and you may find you can get through the entire operation using multiple retries.