Yes. Fraps can record movies outside of games. By default, fraps can record everything that is DirectX or OpenGL powered. Media Players can be set to play the movies through OpenGL or DirectX and when done, you can use Fraps native abilities to record the movie.
In addition, you can record the DWM (Areo desktop) which records everything on screen. Although this is much slower than native game recordings, it will work.
You cannot change the recording area from the DWM device. If you need that, there are other tools specifically for doing that. For instance, I bought Camtasia studio for this sole reason, and Fraps for game recordings.