From a welding perspective: I always wanted to weld up my own pipe and intercooler out of some variation of aluminum. I have the plans for it just no vehicle to put one on. With that said...
An aftermarket ALUMINUM TIG WELDED intercooler will do two things in specific right off the bat. First off, the rapid heat dissipation of aluminum over steel allows the air passing through the unit to stay cooler longer during engine operation. So in other words; metal for metal, size for size, and welded the same way, aluminum will run cooler air to the intake when in operation compared with a steel unit. Secondly, factory units normally have pressed on end tanks. What are end tanks? These are where the intercooler pipes connect to on the one side and on the other side it connects to the core, or "fins", of the intercooler. Again they are usually pressed on for factory applications;however, when you custom make and fabricate ends tanks you always weld them. This allows for not only a great looking piece of equipment but also a more structurally sound piece. So when you do in fact push 80 pounds of boost, like DurallyMax said, you won't blow holes through it.
Surface area of a aftermarket intercooler may be greater then on a stock unit, allowing for air to pass through a greater. Nevertheless the pressure drop (which is the drop in pressure of the compressed air passing through the intercooler) may increase with a great surface area.
Do not forget the location of the intercooler and where it is placed. All locations have there advantages but for drag racing, road racing, or sled pulling a front mount intercooler (FMIC) is your best option. If the stock intercooler is a top mounted, or a self containing, intercooler like ones found on a WRX, Mazdaspeed 3, or the new Corvette ZR1 then switching it to a FMIC can now give these cars a greater advantage of cooler air flowing through the unit. This also applies to side mounted intercoolers, like ones found on older Eagle Talons, Mitsubishi GSX, and older Toyota Supras (1993.5 - 1998). FMIC are the staple in the racing world for most any driving application.
One of two main disadvantages of FMIC are that they add weight up front. This is bad for a drag racer needing the weight transfer to the rear, or the road racer that needs to whip the rear end around turns, and yet it works great for the sled puller that needs the counter weight balance for their truck or tractor. The main, and somewhat obvious, disadvantage of a FMIC is that it typically sits in front of the radiator. This blocks cool air from passing through the radiator fins and then essentially running your engine at a hotter temp. This can, in part, be rectified by designing the FMIC to not be to big as well as mounting it properly so that air can pass through to the radiator.
Lastly, if you are to add a water to water intercooler or a air to water intercooler then you will have even greater cooling properties from the unit itself. This is not recommended to be used on the street by most anyone out there. The cooling properties are limited to the water supply that you carry on board to keep the air cold. Most air to air (which is on a stock duramax unit) intercoolers will work for 95% of the diesel driving population.
**Aftermarket pipes and intercoolers cost big money based on the time and material that goes into making it. Aluminum is not cheap and neither is the time of the TIG welder that has great skill in fabricating a finished product like an intercooler. If you honestly wanted to improve the cooling properties of the intake air then I would suggest on going with a snow performance water cooling kit. This is cheaper then even building an intercooler let along buying an aftermarket piece. Besides I'm sure you will see better gains with water injection on a stock or near stock truck.**
I bet that's a lot more information then you cared to know about intercoolers huh?
Erik
~~~ Will be editing in the morning!! Sit tight and bare with me on this rough draft. ~~~