The difference in transfer cases is all the non-Rubicon model jeeps came with a
NP231 transfer case and from the get go all the Rubicons came with a
NVG 241OR a.k.a. as the "Rock Track" The 241 came factory equipped with a 4:1 lowering gear for better crawl ratios.
Rubicon's also came with standard 5 speed manual transmission, NV3550, and later on the NSG370, you could also get it with a 4 speed automatic transmission with over drive, that has never been an option in non-Rubicon models.
The transmission tunnel or opening was increased in size to accept the larger automation transmission, thus all Rubicons have this feature.
The first Rubicons 2003-2006(?) came equipped with factory installed "air lockers". These lockers were a similar design of the famous ARB's, but activated on a lower air pressure , 5 psi. 2 small compressors were mounted to the transmission cross brace under the skid plate powered the air lockers. These low volume, high psi compressors had a low duty cycle and caused DC some problems as well.
DC changed these in 2006(?) to electric lockers due to the trouble of maintaining a air locker with customers who didn't engage them regulatory to maintain there internal parts.
As Jason said with the rest of the equipment changes there was also some interior changes to the Rubicon models.