I guess alot of that is personal pref.
What engine size?
Trans. type?
Do you have a pref. on the year? (97-late 99 early 00 tend to be close in price, after that, they start going up)
specialty model? Rubicon or Unlimited?
I'll take you through my decision process.
I just bought a 98 TJ 4.0L because I've owned 2.5's in the past and I knew I wanted the extra power and torque of the I-6.
I knew I wanted a Manual Transmission.
I knew I wanted something in good shape (ie, not yet modified and offroaded). Some folks dont care about that, but I wanted to know what all she's been through.
I knew I wanted a soft top or dual tops. From my past experience it is cheaper to get a soft top and buy a hard top later. The only exception is if you have half doors and have to buy full doors.
I wanted full doors, but since I found one that matched my other criteria, I let it slide.