Hi!
We are discussing on Commons list (http://lists.wikimedia.org/pipermail/commons-l/2008-November/004338.html) possible support for Chemical Markup Language (http://cml.sourceforge.net) and Jmol viewer (http://jmol.sourceforge.net).
Extension for MediaWiki is already implemented (http://wiki.jmol.org/index.php/MediaWiki). However it was done for 1.12 and some security concerns exists. Will be great if somebody will review extension code and adapt it to current MediaWiki state if necessary.
Eugene.