Now that I've just gotten my third XJ, and the 6th in the immediate family (87,95, 99 for me, 93 for stepson, 96 for son, 88 for Xwife) I have a few observations:
All years of the 4.0 and the AW4 transmission seem to be good. The first year, 87, did not have the usual first-year teething problems. 91-up cooling systems are a little less quirky.
The Peugeot 5-speed transmissions in the early 4.0's are poorly regarded. The internal slave cylinder is a big hassle to replace, and expensive. But I think the fault of the transmission is more one of toughness than of quality, and in road use they often seem to last all right.
Sometime in the early 90's they improved the brake booster. The brakes on the 87 were pretty poor. By 93 they'd gotten significantly better.
The choice between Renix and Chrysler electronics is pretty much a toss up, but the Chrysler diagnostics are at least occasionally accurate, and that's useful. Both are pretty reliable, the Chrysler sensors perhaps a bit more long-lived than the Renix. My 95 has never thrown a code, but the 93 had a couple, and the codes did help. OBDII starts in 96. Renix engine computers had a tendency to cause FM radio interference. It varies with the radio. I read that there's an upgrade, but it's not a recall: you have to buy the new computer.
It seems to me that mid-year models such as my 95 suffered from slightly less careful body construction - subtly wrinkly panels, poorer fit, and more rust, especially the rocker panels. The 87 and 88 seemed tighter and rusted less quickly. The 99 seems to be beefier, less flexy and rattly off road, and feels bigger on the road.
Some of the earlier Chrysler-era 4.0's have somewhat annoying piston slap. This doesn't affect durability - my 95 is happily slapping away at 260K miles - but the lack of it is a plus. The 93 slaps too. The 96 and 99 don't. The 87 and 88 didn't either.
The post 97 version suffers in some areas of interior accommodations. No door pockets, no little shelves, tiny glove box, no place to put stuff. But it has cup holders.
I never liked the steering column design on the 95, and the intermittent wipers were not as nice as the 87. They changed from Saginaw to Mopar columns in 95, I think. The little horn buttons are virtually worthless when you actually need the horn in a hurry. The 99 is nicer.
The power steering on early 4.0's is overboosted. Nice for parking, but less so on the road.
They redesigned the handbrake in 97, moving the mounting points for the cables, and it's vastly improved. If you drive a manual this is important if, like me, you dislike parking in gear. I love the 99 for this!
If you do not have working air conditioning, an earlier model with opening vent windows is nice. The AC on my 99 doesn't work, and I have yet to see how its vents and windows will work if it doesn't recover with a cheap recharge.
Seats vary with model, but my 87 Pioneer had the semi-deluxe cloth seats with a tilting base. They were the best seats I've ever had. Superb for long trips. Seats changed in 95, and again later, I think. They're tolerable, but not as good. Older power seats are said to be pretty unreliable.
Later roof racks are a little better designed, easier to adjust, and seem less likely to leak.
The steel gas tanks on pre-97 models are prone to rusting out. But the external fuel filter is a plus.
My 95, despite some faults and advancing age, has been about as dependable as any vehicle can be.
uke: 
