Mark, check out "Turbo Diesel Registry" (TDR) for more information on the Dodge CTD. I've been lurking there since before I bought my CTD. The general consensus on the best years is 2004.5 to 2007 with the 5.9L. This is based on my opinion and not supported by any facts I can quote. Keeping in mind the people on that forum are looking for help with problems, what I've seen is a common tread going through the problems. Many of the folks have added mods to their engines and they seem to have more problems then the stock engine folks.
Jay is right. I don't use all the power I have now, why spend money for more? I personally would stay away from a used truck with engine modifications, after all the manufactures have some pretty smart people working for them. If they thought they could increase power and torque with just a "chip" why wouldn't they? There is a trade off.
Like Rich and Jay I think the Ford 7.3 is an excellent engine. The 2005 and 2006 6.0 Fords are pretty much debugged so they would be a good choice to. Same with the GM Duramax. A Dodge Cummins engine with a GM Allison in a F250. Oh baby, oh baby come to poppa!
Cheers,
Mike