Whatever extension syntax we decide on, I hereby officially ask for the support of SMILES. SMILES are a simple (wiki-way!) syntax for describing molecular structures. For a tutorial and examples, see
http://www.daylight.com/dayhtml/smiles/smiles-intro.html
Automatic rendering should * ease the addition of molecular structures to articles * make uploaded structures obsolete (save space/avoid copyright issues/reduce cluttering of image namespace) * unified look'n'feel
There appears to be a toolkit at http://www.daylight.com/products/smiles_kit.html but I didn't look into it yet. There is also a Java app that can render SMILES into PNG, somwhere...
Magnus