Catherine if you count the turning into a incubus ending. That makes it awesome.

Final Fantasy X & X-2 - Yuna/Tidus
Final Fantasy 7: Crisis Core - Zack & Aerith
Moon

Zael and Calista from Last Story, don't really get why that one resonated so much with me because love-stories are usually something i don't care about

Tidus and Yuna (FFX)
Zack and Aerith (Crisis Core: FFVII)
Kanji and Naoto (Persona 4)
Chie and Steak (Persona 4)

Aside from several potential Fire Emblem romances, Super Paper Mario gets my vote.

Claude and Rena from Star Ocean the Second Story BY FAR. Not saying that it can't be your favorite, but if it's not a potential favorite, then you need to play the game. Alan and Cerl from Breath of Fire is a close second.

Others are Zack and Aerith from Crisis Core, Locke and Celes from Final Fantasy 6, Arc and Kukuru from Arc the Lad and Arc the Lad 2. Elc and Mariel plus Elc and Lieza from Arc the Lad 2. Ryu and Nina from Breath of Fire 5. Alphonse and Eleanor from Tactics Ogre Knight of Lodis.

Guybrush Threepwood and Elaine from the Monkey Island series. Classic parody of a witless husband and his wife there.

Tidus and Yuna.

Though I certainly enjoy trying to bed as may females as possible as Commander Shepard.

Most likely Johnny and River from To the Moon

Bastila and Revan in Knights of the Old Republic has been, in my opinion, one of the more interestingly written love-stories. Though, I gotta say, Anyu and Kafei from Majora's Mask are a good choice too!