I just managed to corrupt contents of my Eclipse .metadata directory. Starting up with eclipse -clean did not work out. Deleting .metadata and then importing all projects, plugins and setting does not sound too interesting. I ended up moving .metadata/.plugins/org.eclipse.core.resources/ elsewhere and reimporting my projects only.
Are there any tools or best practices to recover workspace?
I know this sounds obvious, but if I'm writing code for a living I would be sure to do a full backup weekly, with corresponding incremental backups daily.
Simple and easy recovery.
For a simple way to backup your eclipse directory and assuming your using Linux, you could use rsync.
rsync -ar <eclipse-dir> <backup-eclipse-dir>
You can put this in cron and have it backup your files automatically. It will only copy over the changed files to your backup-eclipse-dir on subsequent runs.
I haven't been able to avoid rebuilding workspace occasionally (one or twice over several years of using eclipse). Delete the .metedata and rebuild.
If the workspace is not that big you could backup to say dropbox as a private locked folder.
I have some experience at recovering from eclipse when it becomes unstartable for whatever reason, could these blog entries help you?
http://blog.chris-alex-thomas.com/2009/08/26/eclipse-refuses-to-start-again/
also search for "cannot start eclipse" (I am a new user, I can only post a single hyperlink, so I have to just ask that you search for the second :( sorry)
perhaps those allow you to recover your workspace as well, I hope it helps.