A lot of people have mentioned the difference between the two diesel engines, so I won't get into that, but here are a few other things to know:
The 2005 will have a coil spring front suspension (as compared to the leaf springs on the 1999). This will give it a MUCH better turning radius. My 2003 F450 has the turning radius of an aircraft carrier.
The 2005 model was offered with an integrated brake controller that senses brake pedal pressure and applies the trailer brakes accordingly. It's a much smoother and more efficient way to stop than an auxiliary unit that relies on a pendulum to sense when you're slowing down. IF the 2005 was equipped with it from the factory, it's a nice option to have.
Most folks I've met will agree that the 2005 front end looks better.
The 2005 has a better automatic transmission and larger cooling system for the tranny. The cooler can be retrofitted to the older truck.
If properly maintained, the 2005 truck should get better fuel economy and run MUCH more quietly. I love my 7.3, but it is not a stealthy engine by any means. I have to turn it off to use a drive-thru speaker. Come to think of it, I have to k-turn in many drive-thru lanes as well. Both of those things are good for my diet, as I tend to avoid fast food when I'm in the truck.
2003 F450 Crew Cab, 7.3 PSD "Truckasaurus"
2010 Coachmen North Ridge 322RLT fiver "Habitat for Insanity"
I love my tent, but the DW said, "RV or Divorce"...