Batch video creation. Is there a tool that can do this:

Suppose I have 100 full length tv-shows on my HD. Clips are named BreakingBads01e01, weedss01e01 etcetera.
Is there a tool that can go in and automatically create a 1 minute clip from somewhere in the middle of all of these shows, then spit it out as breakingbads01e01clip.avi or similar? I want it all to happen at once. I do not want to click a button and choose the files 100 times over.

And it would be good if they could all be watermarked in the process as well.

I suppose this feature might be available somewhere in FFMPEG, but that syntax gives me a serious headache.

Any clues people?

You mean encoding? After Effects has a good encoder, but it's an expensive piece of software. For a low-end solution, the free software VLC media player can do this