Basically the tuner adjusts fuel, timing and spark advance settings per a pre-determined set of tune adjustments to the basic OEM tables.
The results of the programmer and the canned tunes are better throttle response, more power earlier in the RPM band, more efficient air/fuel ratios (richens the mix some and removes a chronic lean condition) and overall better driveability. You may even see an improvement in highway MPG.
A custom tune takes it to the next level. Even more throttle response, WOT shift point settings, all taken from logs you provide when you first get the tuner and custom tune program package deal, like the one available from Moe's Performance. Having a tune made with logs from your own truck is like getting a custom suit made for you at the tailor's shop. It just looks, and works, better.
I've been tuning and tweaking tunes using DS products for 10 years on several different vehicles including the LX platform, Ram trucks of the third & 4th generation and GM cars and trucks.
In my experience, I've found the custom tunes are the way to go. There isn't enough difference between what an individual tuner will do and the final product. One may approach certain things differently but at the end of the day, you won't miss out on anything either tuner can provide.
Good luck with your tuning mods if you decide to add a tuner to your truck.