Why are there what looks to me like two mufflers on 06 Hemi D's. There is one long one in front of the rear axle and a shorter one in the after.

 

The one in the front is the muffler the one in the rear is the resonator...
I know a lot of Guys that replaced the rear with a pipe for a little more aggressive sound!

 

Interesting question. I have an '05 and recently had someone hit the rear end of it. It messed up the bumper and the exhaust. When the body shop put the order in for the exhaust, they were replacing from the front muffler back, all they got was the pipe, no second muffler. They had to do some research and it seems Dodge has dropped the resonator.