1. Metal Gear 2: Solid Snake
It would be really fun to see this done in the way of the modern Metal Gear games.
2. Tenchu 2: Birth of the Stealth Assassins
Best story in the series and one my favorite stories in all of games. A remake would bring it to more people's attention.
Often talked about, hopefully it will become a reality.
4. Final Fantasy VII
Another obvious choice.
5. Bushido Blade
For modern physics and graphics.
6. Dragon Force