All the source code for Red Hat/JBoss products is available in opensource (in svn/cvs etc.), but the sold version is what is called the productized version.
What does productized mean ? It means as Michael says, it has additional tests/QA, it is the certified bits, it has matching doc's, etc. It also means that some features in the community version is disabled, removed or have a slightly different configuration default and slightly different packaging.
Examples of differences:
i.e. JBoss EAP comes bundled with Seam, JBoss AS does not.
The productized Seam 1.2 works on JBoss AS 4.3, Seam from .org did not
JBoss EAP has a 'production' profile which is tuned for production (i.e. hotdeploy disabled and other best practices which our support recommend), JBoss AS does not have that.
JBoss EAP gets supported and guaranteed cumulative patches for many years, JBoss AS from .org does not.
All of the above is about having a productized version that is supportable for a long period of time and hence much more about having a stable version than about having the latest-greatest cutting edge version of the latest development.
If you are looking for the bleeding edge then JBoss.org is for you.
To answer you question for Michael, "If I download the code from JBoss.org i'm sure to be using the same stuff that someone who buys it from Red Hat, correct ?" - Then the answer to that is: It depends on the project.
Some projects are exactly the same, where as others have more visible differences BUT all features in the productized version is available in the .org version, but there might be some features that exist in .org that has been removed/disabled (see above)
So what to do ? If you are looking for bleeding edge, use JBoss.org - if you are looking for making sure you are developing on the exact same set of binaries which JBoss/Red Hat can provide development and product support on for the next many years, then the 99$ product from Red Hat you refer to (I assume you meant JBoss Developer Studio Portfolio) is your best option.
btw. the official answer to what the difference is between the community and enterprise (productized) versions is shown at http://www.jboss.com/products/community-enterprise/
For full disclosure: I'm the lead of JBoss Tools and JBoss Developer Studio.