I am wondering how to create new clean Eclipse workspace but having all settings from an existing one. Maybe something like cloning but without projects?
You can have a look at the following plugin : http://code.google.com/a/eclipselabs.org/p/workspacemechanic/
It's a plugin developed by google which lets you store your preferences and apply them to any workspace automatically.
If you store it in your dropbox (or any other shared storage), you'll be able to share you preferences between all your computers and even between all your team members.
It's the best and most reliable solution for your problem.
Best way is to copy the .metadata folder to a new folder and open that folder in Eclipse Workspace dialog box.
I use export->preferences->all then change to a new workspace and import the prefs. Works fine (though clearly not very comfortable). Unfortunately, eclipse only offers to copy the layout settings when changing workspaces which is not enough for most purposes.