The Nov. 2011 issue of JP magazine had a good article on what to watch out for in a used JK. CLICK
1. blown or leaking steering stabilizer.
2. Bent sway bar end links, sway bar brackets, LCA bends, cracks, etc.
3. If the top of the front tires appear angled inward, could be bent inner C's
4. bad ball joints, known to fail with as little as 20,000 miles
5. faded plastic bumpers, fenders, door handles, etc.
6. cracked fiberglass hardtop.
7. thin paint is an issue so look for rust on windshield brackets, door hinges, inside cowl vents.
8. Cheap plastic was used in the construction, so look for: Interior-broken plastic retainers around door panels, trim pieces. Exterior-fuse box hinge, hoses, wire looms. Interior plastic on dash scratches easily.
9. Broken plastic pieces in the shifter mechanism to the transfer case.
10. Broken or damaged evap canister. From factory hangs low between the driveshaft and exhaust. Aftermarket sells a skidplate or a kit to move it above the rear axle.
11. If lifted, look for cracked or torn boots on the driveshafts.
12. If it's a Rubi, make sure the lockers are working. Lockers only activate in 4L.
13. The 3.8L is notorious for consuming oil.
14. Leaking water pump.
15. Water leaks in from roof or doors.
My 2007 with 72K miles has already experienced #s 1,4,5,6,7,8,11,13,14 and 15. But I still love driving it.