Oh, there are far too many favorites to mention. Unfortunately a lot of romances in Anime are not entirely wholesome, let alone have fully consummated happy endings. I can still name a few standouts that come to mind, mostly those that do not devolve to pure romance, but have a good story to go along with the character interactions. A few mentions that I expect few will recall.
Thus I will mention that I caught Akagami no Shirayuki-hime (Snow White of the Red Hair
) a couple of years ago, and thought it to be a very lovely, wholesome sort of romance. And not in any way boring or staid.
I also thought the relationship that arose in the Unlimited Bladeworks
arc of Fate Stay Night
between Shirou and Rin was nice. (Probably even nicer than the one between him and Saber in the original arc -- even though that is supposed
to be the "best" ending.)
But my all-time favorite is from Full Metal Alchemist: Brotherhood
between Ed and Winry. The fact that they have their own paths that intertwine without overt romance, you STILL know they have great feelings for each other and are fated to become a couple, which they do in the very end. (Thank God!
Which is why Brotherhood is infinitely more satisfying than the first FMA series.)