Since our org has been upgraded to Spring '12 I have had sporatic incidents where I try to edit a classes body (not change the class name or delete it), and the API returns an error:
Save error: This apex class is referenced elsewhere in salesforce.com. Remove the usage and try again. : Visualforce Page - .... visualforce page that uses this class as a controller...
I'm not trying to delete the class, and removing it from my Visualforce page would require me to remove other pages/classes/etc.
This error comes and goes, and happens for all classes that are controllers to VF pages.
Some of our classes are part of managed packages, but we're editing them in the org that the package was created out of, so this shouldn't make any difference.
I've had some success using the Migration Tool to move changes from another org, but it also sometimes returns this error.