There are tons of threads on this but try this,
Launch game, open console (~ key) and type these commands one at at time:
Exit the game and open your DoomConfig.cfg file located in your Doom 3/base folder. Alt+F and type custom in the searchbox. You should see a couple commands that say customHeight and customWidth. Manually input your monitor's resolution where the xxxx's should be. So if you have a 1920x1200 monitor, customWidth should be 1920 and customHeight should be 1200. Double check and make sure r_mode is -1 and r_aspectRatio is 2 in your config file.
Launch your game and it should be the proper resolution. Your in-game menu will still say 640x480 but just ignore that because it's a display menu bug.