The above shows a depiction of the first 100 molecules in PubChem, as drawn by Open Babel:
obabel PubChem3D.sdf -l100 -d -xC -O mols_100.svg
Want to see 1000 molecules?
1. If you don't see anything above, you may want to upgrade your browser.
2. Open Babel is not the only Open Source chemistry software with SVG support: there's also the CDK, Indigo, OASA/BKChem and probably others.
3. In the Open Babel GUI, if you tick the box "Display in firefox" it shows these depictions when you convert.
4. One nice thing about SVG is that it can be styled with CSS, so that you could have a button on website that allows you to instantly change the colours of the bonds or labels, or the line-width. I don't think that the Open Babel SVG is set up for these shenanigans at the moment, but it could easily be done.