I know at least one part of it is made with jib jab, but I was wonder if any of you gurus notice a certain program being used, because I think it's pretty impressive and would like to use it.

Looks like just a lot of masking stuff. Voice is autotune which is easy enough to get but takes some fooling around to understand. The more complicated animation stuff I wouldn't try outside of After Effects but most video editors should be able to do the masking with a bit of effort.

I know what masking and auto tune is, and After effects can do mostly everything...

What I'm saying is, from the looks of it, it's just some plug n paste wizard sort of thing being used.

I imagine most of the backgrounds and stuff is stock footage. Once you've built the mask for the dude already you would then just be copy and pasting stuff from thereon, yeah. Take a look at Sony Vegas for a basic idea of video editing like that if After Effects is a bit much to take in (I haven't switched yet because AE makes basic editing horribly painful and inefficient). Nuke is another editor I've heard good things about but, while I have it, I haven't checked it out yet.

Most of the video is really just masking stuff and syncing it. After Effects has motion tracking stuff that lets you sync movements much easier, not sure about Vegas, but it makes things like CGI on RL camera footage trivial (and, incidentally, syncing movements of stuff like this).

The custom animation stuff, if some of it is animated like I think it is, gets quite a bit beyond my league. If it is hand made then I doubt you can do that outside of something like Nuke or AE without a lot of trouble. Alternatively you could be looking at rendering animations out of 3ds max and then using those as a layer.

All of the color effects and film grain stuff and such is all fairly simple filters you get stock in something like Vegas.