Eclipse was unusable, and my workspace seemed to be corrupt. Whenever eclipse tried to write or open files in my workspace I received an error that said the directory was corrupt or could not be read.
I looked around and found at tip that suggested removing one folder from my workspace [1].
Based on that suggestion I removed this directory: $MY_ECLIPSE_WORKSPACE/.metadata/.plugins/org.eclipse.core.resources
That worked for me. When I restarted Eclipse, all my projects were gone, but all my preferences were there. I re-imported my projects and was able to work again.
Eclipse Platform Version: 3.4.2 Build id: M20090211-1700