There are a bunch of names that come to mind. Many already suggested. Savage, Jericho, Punk, Orton all stand out. I suppose there are others. For example, Edge was a solid babyface but his heel work is just so much better. Similar with the likes of Piper, Flair and Batista. It's not as if Shawn, Taker, Foley, Austin and perhaps Lesnar (that remains to be seen) where bad at one of the roles but I would suggest there are two names that are truly above the rest.
Triple H was special in either role. To me, he is one of the greatest heels of all time and his work can still be seen to this day. He is fantastic at getting heat and very few wrestlers have got emotion out a a crowd like Triple H. Indeed, with him being on TV less often, playing a more mellowed character and his reputation off-screen; I think he may be cheered a bit more often. Give him one promo, however, and he will have an entire crowd hating him. Evolution was fantastic. As with the stuff with Stephanie in the early 2000's.
His babyface work was also very good. The work in DX (in different eras) really stands out. How about that awesome run after his injury in 2001. The guy could be a funny babyface but also a bad-ass; for example, him breaking into Randy Orton's house in 09. Sure it is in part due to longevity, but very few wrestlers have offered as much as both a heel and a babyface.
The Rock is an obvious name. He is entertaining as either but I think I prefer his work as a heel. Both in the corporation and when he was Hollywood Rock. Flip that to when he was a babyface and we have him feuding with Triple H or Cena. Again, very memorable and entertaining.
Jericho, Punk and Savage are all fine examples as well but Triple H and The Rock belong in their own elite class. No-one, in my eyes, conquered both roles as well as these men did. Indeed, both were versatile within their realm of heel or babyface further strengthening their case.