As far as code goes, there is none. It's expected that commercial code be written better, but that's not a requirement, just an expectation.
The major difference between commercial and free is the level of support expected. Most sensible people will cut you some slack if the support for a free extension is spotty or slow (some won't, even then). But once you take their money, they expect professional support.
One thing to be aware of when "going commercial" is license limitations. Read the Joomla license (GPL) and understand what that means for the code you write. Since Joomla is licensed under the GPL, you will probably find that your own PHP code will have to be as well (it's the viral nature of the GPL). Understand what that means for you before you start down that road.
(Insert standard "I am not a lawyer but my desk is 20 feet away from one" disclaimer here.)