I can only tell about Half-life 2, just bring up the console by the '~' key (you can enable that in the advanced control options) and type 'cl_showfps 1' and enter. Now the game will show the FPS while playing.
Regarding Doom3, you can do the benchmark by the default timedemo, it will show the average FPS you can get throughout the game. But I forgot the command for showing the real-time FPS.
Just bring up the console by 'CTRL + ALT + ~' and type 'timedemo demo1' and enter.