Thorsten Flügel found a nice speed up for the CDK as part of the work in Dortmund on Scaffold Hunter: calculation of Morgan numbers. He has actually written a set of patches, and analyzed several bottlenecks. I expect more of that work to enter the CDK. Below is my observation of the speed up:
The patch for this has been pushed to cdk-1.4.x now.
Calculation of Morgan numbers is used (canonical) SMILES generation, but also in the isomorphism checker, so the performance boost is probably going to show up at many places. Got numbers? Blog them!