Master of Magic. Fix those damn bugs, add more spells and units, and anything would be an improvement in the graphics department. Keep it 2D, though.

Baldur's Gate
Monkey Island
Day of the Tentacle
Zac McKracken
Ultima
Wizardry

EDIT: Forgot one: Jagged Alliance

"instead of"? No, no, no. "in addition to" would be perfect.

Actually, I'd like to see OoT/MM remade for Wii U as a single product (two games in one) and then Wind Waker remade for Wii U, perhaps with Phantom Hourglass added as a second game on the disc there, to be played entirely on the Gamepad. That way, you'd get good coverage of games, without too much additional asset creation.

Crash Bandicoot 3 Warped

Zelda A link to the past.
Super Metroid
Conkers Bad fur day.

Final Fantasy 3. Maybe thats how Final Fantasy can make a come back.

My favorite most awesome game in the world "Star Con II' or 'Star Command II.' It was the first game I remember that was as deep as a book, fun and action packed, and you could play it different ways and the story would change.

http://en.wikipedia.org/wiki/Star_Control_II

Legend of Dragoon
Xenogears

and...

wait for it..
.
.
.
.
Final Fantasy VII

Hah, I didn't knew that. But yes, Wikipedia says there is a Special Edition of the first two. Thanks for the hint.

Today is your lucky day as Baldur's Gate has also been remade. It released this year on PC an iOS.

banjoo kazooi 64!! i wish that would be remade with new technology, graphics, animation and improved gameplay. i wouldnt want rare/microsoft to make it now though, it would suck ass. but somebody else who would make the game awesome