I vote for Archer/Trip. And Lee/Anders. Forget Petrellicest, I'm all about Peter/Sylar.
Also, Doakes/Debra on Dexter. I was a big advocate of this pairing during the first season - especially with scenes where she went to eat with his folks, and he seemed to somewhat like her, and boy would it complicate Dexter's family life... but, well. Heh.
If they'd taken Doakes in a whole different direction as a character in S2, this could have been very interesting. In the jump from S1 to S2, they could have made him the straightforward bullheaded type, who wants to stop Dex at all costs, or a more subtle and complex type, who recognizes that even if their motivations are different, Dexter and he share common-ish goals. He might have been on to Dexter and not said anything...immediately...
I liked the way they took the Doakes plotline, but it's too bad they couldn't have gone back and done it the other way, too.