One that always gets brought up is HBK/Rock, IIRC there were some huge personality issues that got in the way there that prevented that one from happening.
Kurt Angle vs. Daniel Bryan will probably happen some day when Kurt does his inevitable last ride in the WWE, but if it would have happened just a couple years ago even, it would have been so much better.
Brock Lesnar vs. Austin was supposed to happen, and Austin wound up walking out of the company because he didn't like the way he was booked to do the job.
Lesnar vs. HBK never happened at all either, as far as I can remember.