I have been looking at these off and on for a while now, and just recently kind of back into them again.
I personally was looking for a 2001 to mid 2004 LB7 truck because it had none of the emissions stuff (no EGR, no cat, no DPF, etc), no variable turbo stuff, etc. Seemed more simple to me I guess. The valve cover design made changing injectors more difficult if I remember right, but that's not a huge deal IMO. Granted, they also make the least horse power and torque, but I think it would still be ok for my purposes. Not to mention I have read they were popular because they get a little better mileage than the later trucks, but that could be subjective. Also, they supposedly have the "weaker" 5 speed Allison instead of the 6 speed, but again, for me personally, I don't see that as a problem for my plans. Not to mention, they're older so they're a little cheaper.
I personally see the mid 2004 to mid 2005 trucks with the LLY as a "weak spot" in the production since they upped the HP and torque with the "weaker" 5 speed transmission and then added emissions crap to them. I remember reading the input torque spec for the 5 speed was something like 650 ft lbs, and the LLY trucks were putting down something like 600 stock (verses 500 or so for the previous LB7 trucks). Too close for comfort for me, and no room to "play".
Once you get past mid 05 with the LLY and get the 6 speed, or into the LBZ trucks (06-07) with the 6 speed Allison, I think that would be the way to go. They're the last years before they added the DPF, not to mention more HP and torque, but this time through a "stronger" 6 speed with manual shift capability.
In my opinion, get a mid 05 to 07 truck if you can swing it. Of course, this is all based on what "I've read" and may or may not be true... :D
~T.J.