Grey Fox from Metal Gear Solid and Sephiroth from Final Fantasy 7. I think this was for best "bad guys" in video games of that year. It's been touched up a little from the original since the internet was new back then and I didn't have much reference for Grey Fox. I don't even think he had a name back when the first MGS game came out. He was just referred to as the "Ninja".
Solid Snake and Grey Fox (Ninja) from Metal Gear Solid.
Leon Scott Kennedy (thanks Wikipedia!) from Resident Evil 2.