chuckieland,
You are correct in saying 40fps is about the max that the human eye can see. Some will say 60fps, but it is somewhere between 30-60. However, in many computer games the frames will not stay consistant enough and will dip down below 20fps at times, even when a benchmark shows 35 or 40fps. For this reason, getting a benchmark of 90+fps in Quake3 shows that your machine will probably, under most circumstances not have huge frame drops in most games. If there is a drop, it probably won't go much below 50 or so. Much of this has to do with the type of video card, driver used, RAM, and CPU also.