You want to get FPS scores of YOUR machine, or FPS scores in those game? For Quake, there's a built-in function for that... and as Half-Life is based on the Quake engine (Q2 specifically), there should be a function like that somewhere (but I don't know what it is... Sorry). As for Thief 2, I don't really know which engine is based upon. Maybe Q2 too?
Anyway, if you want to compare those FPS with friends, you should record a little demo with the functions (RTFM to know what are those functions ) and then exchange those demos to see if you're better or worse.