I'm probably going to catch flack for admitting that liked some of the Bioware romances.
Garrus in ME2, because "I've been through all sorts of shit with my friend and we both figured it would be in our best interests if we had sex right now" is a real start to a relationship. I also like that it was the girl (Shepard) who initiated it. And the guy got to be the one who was nervous about the whole thing. Take that traditional gender rolls!
Tali in ME2, for much the same reason, the thing most game romances lack is a believable sense of history, and with the whole of Mass Effect 1 in these character's resumes that's not really a problem. Also Tali is a really good character in general. I could watch her romance the phone book.
Traynor in ME3, Maybe I'm a little biased here but my Shepard had a bit of circumstance that made this choice so natural. I played her from the start as gay, romancing Liara, trying my damnedest to fuck Jack, but settling for Kelly. (and unfortunately letting her get killed by the reapers) But then in Mass Effect 3 Liara was written worse than a dictionary read by Ben Stine. Completely unwilling to do anything but spout off compounded exposition. Then my comms specialist wants to come up to my room and play "chess" with me... Oh, I know what that line means, sure, revenge sex against Liara for not acknowledging my presence I'm all over that. Alright Shadow broker what do you have to say about that!? Nothing... okay what ever.
But then every time I talked to Traynor in the CIC she had something really sexy and clever to say to me and I really ended up loving her by the end of the game.
Now on to some Japanese game you've probably never heard of. (And if you do know about it well done)
Leo and Fyuria from Record of Agarest War, This is the best execution of a Tsundere style romance I've ever seen anywhere. The way those usually work is Girl is a massive ***** to you for no determinable reason, Then half way through the story arc she wants to fuck you for even less reason, and the male character just goes along with it like a brain dead chimp.
In Fyuria's case she has a legitimate reason for distrusting you (You are a general in the army that burnt her village to the ground) And she also has a real tangible reason for warming to you (You treat her with respect and not like some mojo powered douche who thinks sex heals all wounds) Mostly though Leo is just far too good of a guy, somewhat oblivious but far from ineffectual (Which is really good for standard JRPG protagonists)
Sherufanir and Ladius from Record of Agarest War. It's a pretty blatant case of opposites attracting but with the one major boon that puts it above all other attempts at this kind of cookie cutter romantic subplot. Neither party wants to change anything about the other. Ladius is perfectly contented in the passive roll with allowing her to be over the top in pretty much every aspect of her character with out letting it grate on his nerves, while she never once accuses him of being no fun and there fore inferior to everyone who would rather be out having fun. It also helps that she doesn't seem to care at all for Valaria (Who is a very bad example of a Tsundere romance type) At first it seems like she's just fanning the flames of animosity between Valaria and Laduis, but when you figure out that Ladius is catching all the shit from an exchange that he had absolutely nothing to do with you could realize that Sherufanir is just looking out for you by making Valaria reveal her true colors.