There's no reason not to try skype. I was able to get a USB phone to work in an Ubuntu hosted XP guest in vmware but it wouldn't work in Ubuntu.
I've been using vmware server for at least 3 years now with zero complaints.
There's also a new open source virtual machine called virtualbox, but some people seem to have difficulty getting networking set up correctly.
As for ChemDraw, Wine might be an option for you: http://appdb.winehq.org/objectManage...ation&iId=3060
sudo aptitude install wine