Shawn Michaels/Rick Martel at Summerslam 1992
Legacy/Jerishow at Night Of Champions 2009
Angle/HHH in 2000 and Royal Rumble 2001
Bret/Shawn at Survivor Series 1997
Corporation/Ministry in 1999
Ken Shamrock/Undertaker at Backlash 1999
Orton/Edge RAW 07 and Angle/Benoit Unforgiven 02 are the 2 best heel/heel matches I can think of.
Angle/Jericho had a heel/heel match during Y2J's undisputed title reign as well. I think it was the RAW after No Way Out 02. Didn't think much of the match tho, all I can remember is a couple of botched ref spots.
I always thought HHH was more of a tweener than an outright heel during the feud with Angle so I personally wouldn't consider that.
I'm going to be kind of vocal about this. They don't happen often (and shouldn't), but when they do a lot of times it's a decent storyline reason and/or one of them aren't a heel for that match. So you're hardly ever getting a true heel vs heel match.
Randy Orton vs Sheamus (Royal Rumble 2010)- Randy was teasing a face turn that whole match. Cody was the reason Randy lost. So any real heat went to Cody and not Orton.
Legacy Triple Threat at WM26
It was a foregone conclusion Randy was going to be a face by the end of this match. If I remember it was basically a handicap match for a good portion.
The Smackdown MITB match
You had to know someone was turning face by the end of it. Which was Cody.
Angle vs Triple H
If I remember correctly wasn't this part of a 3 way feud? They just had differences of Kurt getting too close to Hunter's wife.
Shawn vs Bret Hart
Bret was a face in Canada and Europe. Not to mention the screwjob basically made Bret face even though he was leaving.