What kind of movies? Mpeg? AVI? FLV? Are you joining a bunch of Youtube Rips? It makes a difference.
For example, here is mpgtx, a simple command line tool that, among other things, joins mpeg video clips. It doesn't work with AVI or other movie file types. So, it would be useless for what you want to do. Thus,, I have no idea if suggesting it to you will work... since I don't know what kind of file type your movie clips are.
Maybe AviDemux is more of what you need. It doesn't operate from a command line, but it does handle a wider range of movie types and it can be automated using projects, a task queue and scripts. Which would mean joining a batch of movie clips, and telling it to add 2 seconds of nothing in between each would not be outside of it's range.
At any rate, Videohelp.com is your friend, as it is a website dedicated to providing it's visitors with everything video... and audio. Editing, that is.