Fraps is good, and its software support has improved a bit recently, but for some games it's still problematic. In particular, it can't properly deal with games that use a dirty rectangles screen update method (this includes all games made with Multimedia Fusion). When I recorded my Mr. Stump's Dentures playthrough (that nobody watched), I had to use CamStudio because Fraps didn't record anything unless the screen was scrolling.
There are generally three things you need to know about using CamStudio:
1. Don't use the "Record from speakers" option. It sucks because it can't detect input properly, it goes out of sync easily, and the "Record from microphone" allows you to do the exact same thing anyway. When using the microphone option, you should set your Windows Mixer (double-click the speaker icon in the System Tray) to record from "What U Hear", or if you don't have that, an option similar to "Stereo Mix". Every time you start the program, it will want to default your recording source back to "Microphone", so you'll need to set it again before recording.
2. Select a framerate that divides evenly into 1000. For example, 20, 25, 50, and 100 are good choices, but 60 is not (1000 / 60 = 16.667). Due to the poor quality of CamStudio's timing code, the recording and playback rate round up to whole numbers, and thus you get extreme audio/video desync due to the two running at different speeds. Using a proper framerate will still have some issues though, since, once again, CamStudio's timing code sucks, and you'll actually capture frames at a lower rate than you specify. It'll still be in sync with the audio for the most part, however. If you're recording about 30-40 minutes worth of footage, sound will be slightly out of sync at the end, but it's nothing VirtualDub can't fix. Just tell VirtualDub to change the source framerate of the video so that the video and audio durations match.
3. CamStudio can't split AVI files. Smart recorders such as Fraps and FCEUltra-rerecording's built-in AVI export know how to split the AVI when it reaches the maximum allowed filesize on the filesystem (either 2GB or 4GB if I recall). Since CamStudio can't do this, it's detrimental because you'll receive an error while trying to save the recording and you'll lose all your footage. Remember that you actually want larger filesizes in most cases when recording, because it means higher output quality. Unfortunately, to work around this limitation you'll need to use a lossy codec. I suggest that you go to the CCCP website and download their codec pack, then use the ffdshow encoder under the video compression options. Then, configure ffdshow so that it uses the highest possible bitrate and have it use either MPEG4 or H.263+ for compression. You shouldn't concern yourself with the other options.