They did this in ToyFare magazine years and years ago. And I never heard anything about lawsuits about it.
Of course it was just a once page shot, maybe several panels, a la comic book style. But same exact premise, toy figures in comic situations. And pretty funny to boot.
Oh, and I found a quote!!
"The toys you use in your stop-motion animation—do you use existing toys, or custom-made toys, or a combination of both? .
A combination of both, depending on what it is. You know, there’s all sorts of complicated clearance processes for getting usage of stuff, but there is some legality under the parody umbrella, which is why “SNL” and “Mad TV” can do the things that they do, because they’re making fun of pop culture or current events, or something very familiar. You know, you have to really demonstrate that what you’re doing is effective parody as opposed to just making Superman a stand-up comic. So, we use a lot, we use some old stuff—everything has to be modified in one way or another, both for legal and animation purposes. But people are going to recognize quite a bit and be excited about it."
Taken from:
http://www.wizarduniverse.com/magazines/toyfare/TF20050112-green.cfm