Well Aperture needs alot out of the graphics card so adding another GB of RAM in the form of a 2GB chip would slow down the performance of the program but keep more RAM free for use in other areas. If you look at the performace benchmarks at
OWC you will see that when it comes to graphics card intensive application the 2GB actually outperforms the 3GB.
So if you just want to be able to use other programs more efficiently then the 3GB is the way to go as long as you don't mind a slight performace decrease with Aperture.