My anecdotal experience talking to JGC owners is that while the engines and drivelines aren't too bad, it's mostly everything that's attached to the them. Front end parts fail frequently, AC systems are in need of constant repair, emissions related items are headaches, and so on.
When you consider the MSRP of a late 90's Jeep GC, they should be priced higher than they are. They were a fairly high end SUV when new. Pathfinders are priced higher, but I bet it's because they're much better in terms of operating costs. Toyota 4-Runners are priced higher yet, and I'm not sure if they're worth the premium over a Pathfinder. When I see what my neighbours paid for a 2001 Pathfinder about 5 years ago, and the superb reliability and low operating costs they've had, I don't see why they don't hold their value better, but oh, well, that's fine for those of us that buy used.