I havent checked out the 2009 version but in the 2007 version of Commerce Server, there were just too many painful things not least of all the whole "Pipeline" framework, which for me, was just too cumbersome to work with.
I am afraid i didnt like commerce server 2007 much..and honestly, even from a MS perspective, it feels like its treated too much like a step son to want to even invest the time and effort to learn a product like that.
This impression of mine is based on my attending the Commerce Server Airlift in 2007 in Redmond which frankly was way less than impressive
There may be Commerce Server sites out there but honestly, i personally think that if you have a choice, you should probably look at something like Magento. I have worked on it a bit for a friends store and i must say that i felt it was probably WAY easier to get it set up out of the box than something like commerce server, in my experience.
However, it does involve knowledge of PHP / Zend etc which may mean a steeper learning curve.