Support for 3D-rendered molecules on Wikipedia has been on the wishlist since ... forever. This was never done due to security concerns, IIRC.
I just found this site : http://alteredqualia.com/canvasmol/#Penicillin
3D molecule rendering completely in JavaScript using canvas. Since it only runs in the user's browser, Wikipedia servers are not at risk; we'd probably have to check the code for potential XSS problems etc., and add a wrapper with a fallback to our normal PNG for non-JavaScript browsers and, yes, old IE. But so what.
Any takers? Or should I give it a go?
Magnus