I prefer Relena and Heero together...but here are my alternatives:
QuatreXRelena=It works...their fathers were both assassinated, they are both reasonably wealthy, and they are pacisfists.
DuoXRelena=That also works...but I can see him in the "Heero dies" or "Heero the abusive boyfriend" fics.
I have also read a couple TreizeXRelena fics. Which is a little creepy...him supposedly being 24 and her being 15...supposedly anyway. But then again, Une is supposed to be 19, Treize must like young meat.

Not sure if they would work as a couple since he is kinda the villian, age differences, and the fact that he does die at the end of the series. However, it could work if it was written as a "what if" fic. I love WIFs ^_^ But then again...I can see the relationship being kinda a forced relationship...such as an arranged marriage, or Relena making a negotation with Treize that she pays dearly for to protect Sanq Kingdom. I can also see it as a non-consensual pairing...*dodges the rabid fangirls hurling of knives and food* As I said...can't really see it working out too much, cause Heero will try to wisk Relena away from Treize anyway. :razz:
Then of course is the controversy of whether or not Trowa and Catherine should be a couple. In the manga "Episode Zero" Trowa is Catherine's long lost brother...in the series Catherine said that Trowa is like her brother. To be on the safe side, I personally wont write a Trowa/Catherine fic just to be safe. But that doesn't mean I wont read Trowa/Catherine fics. :razz:
Quatre/Dorthy? Hmmm...not too sure on that. Seriously that chick needs to wax those babies she calls eyebrows. *shudders* Oh...not that that has anything to do with the pairing. Anyway, reason that I'm not so sure...they didn't really have much interaction other than fighting each other...and she DID stab him, but then again she was sorry for it.
Edit:
As sick as this may sound...has anyone ever run across a Zechs/Relena fic? I think that would be both disturbing..yet interesting read to find. I mean...he DID kidnap her. Sometimes you never with animes these days, I mean Angel Sanctuary had an incest couple...not saying that Zechs/Relena would work out...it's more out of the curiosity of the unknown. I'm such a curious creature.
Edit 2:
Also, I dont mind a OCxCanon pairing as long as it's somewhat believable...I have dreamed up a character that I was thinking of pairing her up with one of the canon guys. Either Duo, Trowa, or Quatre...Wufei, him being a bit of a male chavinist is kinda outta the question...and definitely not Heero! To me...writing a pairing other than Heero and Relena is sacrilige. And I mean...me writing Heero being paired up with someone other than Relena...me writing that personally...not other people who write that. I commend your courage if you're able to write that...I just couldn't bring myself to do that.