I have a clutch that squeak...there's a TSB out for it as a sommon issue with JK's, but the dealer refused to look at it. I'll just run it until it starts causing real issues, and then replace it with a better quality clutch. It can't be that big an issue, since I've already got 85K on the Jeep.
I did have an issue with my steering position sensor and wireless control module, but that was covered under warranty. Airdrie Dodge handled the whole thing well - courteous and professional.
Other than that, my problems are as follows:
My rear bumper is dented (trail damage), my left rear fender is loose (trail damage), my passenger door is creased (trail damage), my license plat holder is crooked (trail damage), and my left upped ball joint is going...which isn't that bad given that I've got 85K on it.
As far as work on your JK goes, if they're covering it all under warranty and not arguing about it, count yourself lucky. It's inconvenient to have your Jeep in the shop, but if you can show the service manager that you've had your new vehicle in his shop for an excessive number of days in a short period of time, you might be able to convince him that he should help you out with the cost of a rental.