A couple of suggestions: for Fraps, try toggling your V-Sync settings. I vaguely remember that Fraps doesn't like V-Sync=Off. For GLide FPS, you could try Unreal/Unreal Tournament. There's that "fly over the castle" timedemo thing you could run.

V-Sync does not seem to matter. I know games with built in benchmarks, but I want to test a lot more. Unreal ironically seems to be the only exception were fraps works.
I am sure there was some other fps logging software for windows 9x.