Can anyone tell me how I delete obsolete JSFiddle versions, but keep the base version?
You want to reset the code to base at the version you're editing. To do this you simply set the current version as the base version with the "Set as base" button shown below:
You can create a new Fork, which essentially does what you want by creating a new jsfiddle from the current revision, though you'll get a new URL.
Otherwise I do not believe there's any method to remove any specific revision or to clean up the revision history of a fiddle.