(not that I'm a big fan of PER, but I can't think of any other measure at the moment)
If I wanted to do a quick-and-dirty comparison, I'd probably use WS/48, although I can see how some people might doubt a metric that has JO midway between Nene/Amare Stoudemire and Channing Frye. Players listed at basketball-reference.com as C, F/C, or C/F with 20 or more minutes per game who have a WS/48 worse than Jermaine O'Neal (who is 26th out of 33): Channing Frye, Andrew Bogut, Byron Mullins, Kendrick Perkins, Mehmet Okur, Chris Kaman, Boris Diaw.
Among those 33 players (not all of whom are actual centers), O'Neal is 31st i PER, 24th in total rebounding percentage, 6th in block percentage, 29th in offensive rating, 7th in defensive rating.
If you drop the threshold down to 15 minutes per game, Jermaine O'Neal is also performing better than Timofey Mozgov, Anthony Tolliver, Aaron Gray, and Darko Milicic (who is averaging under 18 mpg despite starting 20 out of 21 games) according to WS/48.