There is also a BIG difference between the two that isn't first apparent. As Steve pointed out, HomeSeer has many "plugins" where the author has long disappeared, and I suppose that is true for CQC as well, but there is a GIANT different between the two; HomeSeer plugins are locked code which only the original author can modify and make bug fixes to. If an author "disappears" and you have a bug in that plugin or you want to add a feature to that plugin, your basically out-of-luck. So not only does HomeSeer sell these plugins, but you may be buying something nobody supports.
On CQC, with a very few exceptions, CQC "drivers" are completely open, you can view and modify the code, add features, etc. with not that much work. And CQC drivers are quite a bit easier to write.
This may not seem important, but it really is. Equipment that the drivers connect to change all the time, so if a new XYZ DVD player comes out, but the driver only exists for the lower model, then its fairly easy in the CQC world to update that driver. On HomeSeer, you need to track down the author and just pray he will be motivated to support your new model.
Over the years I've modified several CQC drivers to add features or fix bugs and its not all that hard.
This is probably the most important difference between the two system. I agree that it is a huge difference. There is basically a "cottage industry" that has popped up around Homeseer were people make money designing plugins. The end result is there might be more plugins for Homeseer, but you are totally dependant on those plugin developers. If they drop off the face of the Earth, then the end user is stuck holding the bag and ends up having to buy yet another plugin with no promise that it won't happen again.
As far as I know, there is only one CQC driver that is locked down. One of the lighting control drivers. It is only locked down due to a non-disclosure agreement. The manufacture eventually ended up releasing the protocol to the public, so it probably wouldn't take much for Dean to get the NDA agreement dropped should that ever be needed.
EDIT - see Deans post below for a full disclosure of what is currently locked down.