FRAPS does hook into everything (including Firefox, btw. You may check with youtube.com fullscreened vids with ffdshow installed, counter shows and sshoting available).
To alleviate such a concern, maintaining a small withlist/blocklist for the fraps process is as optimal as it gets (allowed only in the games currently installed, and obviously blocked from dev softs, debuggers and similar stuff, though just preventing interprocess memory access rights sounds as nice).
Quite offtopic, btw.
Last note:
ZD Recorder is a very good alternative to FRAPS worth considering. Seriously, why was Hypercam even mentioned??