I'd think I'd go for heels, because, as PauLwall said, face champions (e.g. John Cena) can become tiring and tedious. At the moment the championship holders look like this:
Cruiserweight: Gregory Helms, Heel
Intercontinental: Jeff Hardy, Face
United States: Chris Benoit, Face
Womens: Undecided, though my tip is Lita, Heel
WWE Tag Champs: Brian Kendrick + Paul London, Faces
World Tag Champs: Spirit Squad, Heels
WWE: John Cena, Face
WHC: King Booker, Heel
ECW: Show, Heel
Heels = 4/5 Face = 4/5
So it is now even. However strong indications point to more face champions. Batista will eventually win the WHC from King Booker. RVD will become the ECW champion, Crime Tyme/Ric Flair + Legend will be World Tag Champs and Matt Hardy will become the Cruiserweight Champion.
Then it would read:
Heels = 1/2 Face = 7/8
No this may not happen all at once, but it could. WWE is certainly leading towards a majority of champions being faces. 7 or 8 faces 3 shows! Boring. Heel Champions are fun to watch, and infuriate you (or me anyway) by cheating to win. Sure, kids love Cena and Batista and Matt Hardy, but some of us understand the heel/face pattern, and don't. No offence to any of the aforementions fans, but I just don't think that that many faces is a good idea.