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I would also cast a vote for Shadowrun, but it would be VERY hard to pull off right.
Harry Potter Online was actually started by Origin Systems and was later canceled. They were also working on Wing Commander Online (which would be a helluva thing!) I think most of those guys ended up working on Jump to Lightspeed, or whatever it was called, for SWG.
Otherwise, I dunno. Hopefully Elderscrolls Online is being worked on. If Rockstar made a next-level MMO out of GTA, that would probably be pretty amazing.