If you are talking about making an exact copy of the original game but with fancy modern graphics, then there's nothing really that comes to mind because I'm not that arsed about graphics really. If the game is a classic and I'm not playing it any more, it's because I played it to death and new graphics wouldn't really help.
If you are talking about making an actual modern version of it though where it modernises the game play as well as the graphics, then..... I would probably have a list about a mile long Stuff like:
Omicron Nomad Soul
Jones in the Fast Lane
Hidden & Dangerous games
Tex Murphy games
Space Rangers 2
Summoner
Dune (the original not the RTS one)
Eye of the Beholder
Police Quest
Castles (it would be more than an RTS - it would elaborate on the King decision making stuff too)
Elite
Midwinter
Stunt Island
(yes I'm old)
You could slow that down if you wanted to ya know? There are various little things you can do to do that.
Do you know about the fan made Wing Commander game due very soon, made with the Freespace engine? It seemed decent. I played the first mission which was released as a demo a while ago. It might even be out by now. It's basically like Wing Commander.. but with a nice looking up to date Freespace engine.
*drool*
You ever played, Lock On: Modern Air Combat? It was so good it made me air sick sometimes - seriously. Also, check this out:
http://www.digitalcombatsimulator.com/
There is a lot more than meets the eye there.