If your eclipse crashed and refuses to start, saying something along the lines of: Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown, then try the following.
$ rm -rf YOUR_PROJECT_DIR/.metadata/.plugins/org.eclipse.core.resources
Start eclipse. However, all your projects will be gone.
You can import them via File -> Import -> Existing Projects into Workspace; then select the directory where you had your projects.
EDIT: I just found a better way. (source)
$ rm YOUR_PROJECT_DIR/.metadata/.plugins/org.eclipse.core.resources/.snap
This way you do not need to reimport your projects.
ANOTHER WAY:
As IGx89 suggested in the comments, you can also try the following:
$ rm YOUR_PROJECT_DIR/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
http://stackoverflow.com/questions/11310970/eclipse-juno-doesnt-start/12045547#12045547
$ rm YOUR_PROJECT_DIR/.metadata/.plugins/org.eclipse.core.resources/.snap
$ rm YOUR_PROJECT_DIR/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi
In newer versions of Eclipse, the .snap is called n.snap, where n is a number. My file was called 9.snap.
After I removed it, Eclipse loaded my workspace successfully.
deleting /.metadata/.plugins/org.eclipse.core.resources/.projects//.indexes
solved the issue for me