I don't have to do emission tests, but I use a Smarty SR, and it has a tune just for emission tests, if you have big injectors and such. Also stock tune is still there. Takes a min or two to change tunes.
I have a stock trans 48RE, and have had the Smarty for about 100k miles. It has improved my mpg significantly. Average of 3 mpg better. BUT I didn't buy it for MPG. I don't beat on the truck much, but if I break something, which I haven't yet, I won't be crying how my DOdge is a POS.
If I had a new truck, I wouldn't bother with a tuner, but then again, I wouldn't bother with a diesel either.