The most important thing is how it was maintained. 2000 and 2001 Jeep Cherokees with the 4.0 engine have a cylinder head casting that is a bit weaker. If the Jeep has been overheated, these year Jeeps are more likely to crack the head. This isn't a deal breaker, since the head can be replaced with a beefier one for ~$600 if you do it yourself. I made a thread about swapping mine and its in my signature if you want to take a look. Not all 2000 and 2001s will crack the cylinder head, and many of them don't. It is all about maintenance.
The most important thing about Cherokees in my opinion is the condition of the body. Engines can be swapped, axles, etc, but body rust is what kills these things.
The 2000 has a front axle that isn't the best if you plan on lifting it above 3.5", but it all depends what you want to do with it. If you want to keep it semi-stock and use it as a daily driver, the Limited trim is certainly very comfortable.
There are people on here who will say "blah blah is the best year" but it is really dependent on the vehicle itself. 1999 is a popular year, but I've seen them be total nightmares due to neglect and lack of maintenance. The newest Cherokee is 13 years old now, and with any used vehicle, the service history will be what makes the difference between a good vehicle and a bad one. The goal is to find the best maintained Jeep with the least amount of rust, the year doesn't really matter in this case. If it is in good mechanical and cosmetic shape I would definitely consider purchasing it. They are fun vehicles to own and can be extremely reliable. I've owned mine for almost 6 years now and I wouldn't trade it for anything.