Chrono Trigger. Please, Square, if you're going to put an end to the development of a fanmade remake, then at least make your own. <.< It'd be awesome to see this game in 3D or to see a 2D remake for the DS.
Lufia II: Rise of the Sinistrals. Yeah, it's not going to happen, but a man can dream. =P The Lufia series was (sadly) never that popular, but awesome nonetheless and I would personally love exploring all the dungeons and solving the puzzles in 3D. I wouldn't say no to a DS port for this game, either.
Pokémon G/S. Shiny Gold is good, but I'd like to see an official remake of the games.
Seiken Densetsu 3, once again, I'd like to see this remade for the DS.