The Marine Commander is the protagonist of Final Doom (specifically mentioned in TNT campaign story). He is often thought to be the same character from either Doom (B.J. Blazkowicz (Doom)), or the Marine Corporal from Doom II (who has obviously gotten a promotion or two). Alternatively he could just be another character altogether.
The ending of Plutonia suggests that he has grandkids or will have grandkids. This is assuming he even dating or has children.
Behind the scenes
Prima's official strategy guide for Doom 64, suggests it is the same Marine from Doom II, and that its likely the same marine from Doom 1/Doom 64.