In terms of Apple's own software, such as Aperture, OS X, iWork, etc. there's no difference between the education discounted version and the full retail version. Software from other manufacturers is sometimes a different story. For them the "education version" might mean an inexpensive but limited feature version, and for others it might mean the full feature version but doesn't count towards any future upgrade priced version.
For instance, if you buy a music sequencer at version 3.0 from a retail store for $400, then when version 4.0 comes out you're offered a special upgrade price of $100 to go from version 3 up to version 4 rather than having to spend $400 again just to get version 4.
So it all depends on the manufacturer. Before purchasing do your homework on what the "education" moniker means to that specific manufacturer.