The ingame cutscenes are just scripted sequences using the game engine and thus unviewable outside the game. The prerendered cutscenes are .roq files. I think Raven's toolkit has a tutorial on making them and the program necessary. The existing videos you can replace with any .roq movie you create. To eliminate a video entirely, just rename a blank text file to the name of the video you want to get rid of and pak it up. They're in Assets0.pk3, /video/, *.roq.
Grab the toolkit off Jk2files.com.
Here's a tutorial if the tookit doesn't have it: ROQ Tutorial