I have a 2005 Chevy Duramax with 46000. I am getting around 13.5 in City and around 17 - 18 MPG on highway. Everything on it is stock. I wanted to try to get a programmer for MPG only. I wanted to know what would work best for my application and what MPG increase I would probably get. Thanks

A tuner for low cost I would recommend a Hypertech or the Predator from DiabloSport. I have used both and have nothing, but good reviews about them. Here is a good link about the 2 of them compared.
http://www.dieselplace.com/forum/showthread.php?t=103075

Fuel economy is strictly related to how you drive. To get the best fuel mileage you have to drive like there is an egg under the pedal.

There is a lot of options as far as progrmmers out there and even more opinions as which are the best. Grab a beverage and you can read all day. The gist you will see is some type of programmer or tuning program, opening up the exhaust, and incresing air flow will be the usual enhancements you will see.

Usually with the addition of programmers, exhaust systems and other enhancements comes the urge to play more and hence lower fuel economy. So this may work adversely to what you are trying to accomplish.

I personally have an Edge/Attitude, 4inch TTS exhaust, Cat delete pipe and use the stock air filter and airbox but have installed the TAI Airbox seal kit. I don't drive my truck hard and use a very low power setting for the Edge usually level 2 or 1 if I am towing my 5th wheel.

Depending on time of year with ambient temps I see aroung 17-18 local driving, 20 highway and 10-12 towing 10000lb+ 5th wheel. Winter temps and winter blend fuel I will see about 1.5 mpg drop.

Sorry so long but just my opinion to your question as you will see there are many.