IIS can sometimes be a problem if it's part of the original issue. Another potential problem is related to the Windows architecture that supports SharePoint. If you plan on having multiple Web Front-End servers and using Windows Load Balancing to tie them together, you will likely have problems unless you delete and recreate the virtual Network Cards on the virtual servers. Otherwise there are conflicts between the cloned cards that cause the load balancing to not work.
However, I don't have any SharePoint-specific problems that are common on virtual servers. It usually plays very well with the other children…