Well I'll start with my very first couple:
Hideki Motosuwa & Chii from ChobitsThese two are pretty much where I got my start. I suppose you can debate whether or not Chii is a female or a machine, but isn't that what the whole show is about?
Next up is the more recent:
Ryūji Takasu & Taiga Aisaka from ToradoraI think this was everyones favorite couple from last season.
Another couple worth mentioning:
Kraft Lawrence & Horo from Spice & WolfAs the show progresses this interspecies relationship continues to develop, with both sides unsure of what exactly that may mean.
My favorite couple for just plain Love/Hate relationship:
Sousuke Sagara & Kaname Chidori from Full Metal PanicWill Sousuke live through their relationship? Inquiring minds want to know.