I just recently responded to a thread asking advice on PC games and while I was compiling the list it kept getting bigger and bigger. There were so many great PC game and to a lesser degree there still are today. 

Games I Miss and Want in HD

PC

System Shock 1 and 2

Never Winter Nights

Baldurs Gate

Grim Fandango

Dues Ex

Icewind Dale II

Asheron's Call 2

Max Payne 1 and 2

Medal of Honor Allied Assault

X-Com UFO Defense

Ultima 2 

Starcraft

Doom

Star Wars Tie Fighter

Diablo 1 and 2

Wing Commander

Home World

PSX

Final Fantasy VI

Final Fantasy VII

Final Fantasy VIII

Xenogears

Vagrant Story

Lunar Series

Grandia

Tobal 1 and 2

Suikoden Series

Metal Gear Solid

Syphon Filter

Resident Evil 1-3

Chrono Cross

Dragon Warrior VII

SEGA

Crazy Taxi

A Good Sonic Game

Power Stone

Phantasy Star 1-4

Castle of Illusion 1 and 2

Panzer Dragoon Series

Gunstar Heroes

Jet Grind Radio

Aladdin

ESPN 2K5

Streets of Rage

Shining Force

Comix Zone

SNES

Chrono Trigger

Super Metroid

Zelda Series

Secret of Mana

Mega Man X

Mario RPG

Mario Series

Contra III

Toy Story

Ogre Battle

That is just a preliminary list but there is so many good games deserving of the New Super Mario Bros treatment. Let me know your list and preferably what you would like to see in a remake or sequel to your game of choice.

Very Nice List I would love to see some of those in HD.

1.FFVII
2.FFVIII
3.MGS

4.FFX(Although Very Beautiful Already)

A New Powerstone game would be awesome especially with 4 player at home and online multi player. I think Final Fantasy VII remade to look like the advent children film would blow peoples mind. The again could you imagine Link running off the Heavy Rain character engine in a remade Ocarina of Time with online competitive multi player, I know you want some awesome fishing, and a gladiator like stadium for one on one battles.

I tried to leave off PS2 games cause the graphics are generally high quality but since I added some good looking PC games feel free to add any game you would like.

I personally think that games rule just fine without HD, but to each their own.

Fine than what game would you like remade the most?

Pretty much all my favorite games from the past generations...

I'm only now playing through Zelda: TP (you won't believe my reason, but it's good) and I can't help thinking that HD visuals really add to the immersion of the player.

So, Zelda:TP then.

On the other hand, Metroid looks BEAUTIFUL even in HD, so I could only imagine what Retro would be able to do with it in HD.

Metroid Trilogy for sure.

Oh, and every single Mario game too :P

Aren't most of those PC games already in HD?

I could imagine Call of duty on the crysis engine allied assault was excellent