The folks at the EBI have been doing some great work on the CDK. A major effort is underway to revamp JChemPaint and part of this involves improving the rendering of 2D depictions. While not complete I rebuilt a version of the CDK 1.2.x branch with the latest rendering code from the jchempaint-primary branch and updated the CDK web service. The results are much nicer, though there’s scope for improvements. See for example

http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1

http://rguha.ath.cx/~rguha/cicc/rest/depict/C1CCCCC12CCCCC2

http://rguha.ath.cx/~rguha/cicc/rest/depict/CC(=O)OC1=CC=CC=C1C(=O)O

http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1CC=CC%23N

Thanks to Gilleain and Egon for pointing me in the right direction. Anybody using this service should see the new depictions automatically