I don't think any year is particularly "bad". Things to consider, however;
- 53 block - prevalent from '98 up until 2001, but most common in '98. 5 - 99's
- NV-5600 availability started in 2000, but recieved a larger input shaft in 2001 and is a more desireable transmission (especially for towing) than the NV-4500 which has the 5th gear nut issue as well as not being as strong.
- 2001. 5 debut of rear disk brakes makes the 2001. 5 and 2002 trucks more desireable.
- late 12V trucks ('96 - 98) with the 215hp P-7100 inj. pump are highly sought after though you lose the NV-5600 and rear disks weren't available yet and unless you get the 98 12V then you get the ext. cab rather than the Quad cab.
- as far as third gen trucks go, there aren't any bad years IMO. You'd want to run it up to 75mph to check for vibration, there was a TSB for a revised pwr. steering hose to combat buzzing in the steering wheel and/or pedals and very early '03's had some clutches with springs that were too short leading to noise (not a performance issue though).
- You can do a search and read lots about the comparison of the '03-'04 305/555 engine vs. the '04. 5 and '05 325/300 or 325/610, but I don't think you can go wrong with either truck.
Depending what you want to spend, my favourite 2nd gen is a '01. 5 or '02 3500 dually HO with the 6spd. The 2001. 5 still had the CAD (center axle disconnect) if you care.
Good luck,
Dave