Top three? What. :| Small-time thinking!
But I'll play by the rules.
1. Super Smash Bros. Brawl (Wii)
2. Star Ocean: Second Evolution (PSP)
3. Kirby Ultra Super Deluxe (DS)
So basically a sequel to my favorite multiplayer game, a remake of my favorite single-player game, and a remake of my favorite action/platformer.
And here's my illegal extension to my top fifteen.
4-12. Advance Wars: Days of Ruin, despite the darker story (DS)
4-12. Dragon Quest IV (DS)
4-12. Dragon Quest IX, despite the 3D models (DS)
4-12. Star Ocean: First Departure (PSP)
4-12. Tales of Rebirth (PSP)
4-12. Tales of Innocence (DS)
4-12. Dragon Quest V (DS)
4-12. Dragon Quest VI (DS)
4-12. Tales of Symphonia: Knight of Ratatosk (Wii)
13. Castlevania: [Noun] of [Emotional State] (DS)
14. Fire Emblem DS (DS)
15. Star Soldier R (Wii Ware)
I ranked 4-12 approximately, but really they're infinitesimally close to one another and it's just about impossible to say--and the exact ordering has changed many times. Of course, this may have to do partially with the fact that we're dealing with nine different games but they're only spread over four different series, one of which (Star Ocean) was a sort of spiritual successor to another (Tales) anyway, but hey.
Also, I've played none of those remakes except DQIV; DQV, DQVI, Tales of Rebirth, and Star Ocean 1 might as well be new to me for the purposes of my own experience.
Oh, and yes, if you don't know me, I do happen to love portable gaming, 2D, and RPGs.
Top 15 Tally:
2D games - 13 (including games that use 3D models but play in 2D)
Portable games - 12
RPGs - 11