It’s a good question, and one I don’t have a definite answer to. But I assume the graphics are probably made in something like Photoshop or Illustrator, and then animated in something like Adobe Premier Pro or Apple’s Final Cut Pro. There are also add-ons for programs like these for creating various effects. But I’d also be interested in what other options there are, as it’s something I’ve been wondering about too. I’ve watched a few videos on these programs and seen them do some of these things, but I’m sure there’s more to it.
All of the pros will tell you Final Cut by Apple or Premier by Adobe. I think you should invest in those and learn via tutorials on how to fully edit material for publishing.
I am sure both have 30 day trials. Try them out before purchasing of course.
Final cut pro and premiere are editors, not motion graphics applications. There’s no way you could produce that video in either of those singularly, as their primary function is editing clips, but they only have very basic facilities for animation and creation of graphics.
At a quick glance in that video there are scripted counters, boned animation, shutter blur and 3d camera movement - you could animate the graphics in Flash (good animation tools and scripting) and composite the result in After Effects (proper camera processing). Other options are apple motion, autodesk combustion/smoke, eyeon fusion.