Welcome to the Forum.
You'll get a lot of different answers because this question is a lot like Ford v. Chevy, auto v. manual, etc. I'll try stay unbiased and give you some info to work with.
1988-1995 is the YJ, look for '91+ 6cyl to get the reliable fuel injection. Make sure a manual transmission shifts smooth. Leaf spring suspension is a little rougher riding than later coil spring models. Interior more utilitarian.
1997-2006 is the TJ. Again, the 6cyl is a preferred model over the 4cyl. Don't discount a 4cyl model if it suits your needs, they're reliable. Coil spring suspension rides better than earlier models, interior a bit more car-like. Again, make sure a manual transmission shifts smoothly.
2004-2006 you could get a TJ Unlimited with is longer than a TJ. More rear seat legroom and more cargo area behind the rear seat.
2007+ is the JK and likely over $10,000 still. Wider body, more interior room, coil suspension, weak mini-van motor until 2012.