Oh man, where do I begin? XD There are so many I lost count.
RatchetxTalwyn: I think people knew about this for a while now, so I'm not going to get into too much details. I just think out of all the girls that Ratchet knew/hooked up with, Tal has the most in common with Ratchet.
Ace HardlightxAngela Cross: Ok ok, I know these two never meant in anyway in the games but if you think about it, it can work well. With all the crap Ace has gone though and I'm sure with the lack of people trusting him, if he finds that one girl that may understand him, I think that would kinda boost his mood a bit. I'm not saying Angela would be that girl, but I do see it working.
NefariousxGears: It's cute XD Yeah, Gears is a b**** and is attractive to Money and/or Power (which Nefarious at one time had the latter), but putting that aside, it is kinda cute in a charming yet weird way.
NefariousxVorselon: Eeyeah…Ok, long story about this one. At first this was nothing more than a crack pairing but these two sadly grew on me as a real full time pairing. I don't know, it's just… weirdly adorable to me. Both are over the top, silly and seeing Vor being bossed around by Nef just makes me lol.
I have more, but I'll be all day if I keep going.