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.
1"Merging" in the sense of appending them to one another? I'd probably recommend just creating an empty "black screen" video and then inserting that in between. – slhck – 2012-05-17T12:22:55.260
@slhck: that's good idea, but how to add a single file between every two different files? – Kushal – 2012-05-17T13:56:46.530
Well, you're gonna have a list of files, I guess. Just insert the blank video between those when feeding this list to your batch. See also: Command-line video editing in Linux (cut, join and preview)
– slhck – 2012-05-17T13:57:44.610