It's an interesting idea. Technically, the graphics could be improved if a graphics card was taking the load. A higher framerate, smoother rotation and camera moves - none of this needs the CPU (much).

But there's some computation that can't be done by the gfx card. As far as I can tell, the difficult bit is generating the mesh for each step (since each step is different).

Probably the hardest part would be determining if the graphics card is capable of doing it without bogging down the CPU.

For AutoDock, it would be even harder to make interesting graphics.

I'm sorry I'm not sure I was clear : my idea is to give the option of using a prerecorded animation, not the showing the explorations of Rosetta but a known unfolding, in accelerated (e.g. lasting ~1min). (or 20 unfoldings to make 20 min).
I must confess I don't know whether CPU would be needed for this, but it could be nice, once in a while, to make people curious and convince them to crunch too.
(of course you should eventually explain it's accelerated =)

Do you know if this kind of prerecorded animation would slow the CPU down ?

but retsof is right, I don't know whether it would be useful : at home you can explain to your guest what the WCG is (and show them an animation), at the office if you are running Rosetta it's probably running on all the computers already (?).
Maybe this could help convincing employees to crunch at home, or customers (if they can see it).

just a little idea =)