If you are building lots of free sites on one domain. Example:
www.mydomain.com/sites/site1
www.mydomain.com/sites/site2
www.mydomain.com/sites/site3
Making some kind of hub structure for
www.mydomain.com is definently benificial and will keep all of you sites spidered.
If you only have a few domains on one IP and get into some heavy crosslinking - I would advise against that.