I put line-x in my first JT and my second JT has the factory spray-in. I'm a big fan of the spray in like line-x because of the ability to toss whatever I want in there without worry of damage to the box (scratches turning into rust, etc.) and then I just hose it or sweep it out without worry.
I've got the Rhino liner in the bed. But this thread reminded me of an outstanding project yet completed- the rubber mat. Just ordered the Rough Country mat (thx @22jtrd for that picture).
Liners are great, protect the bed very well. Only one problem I have from time to time... items carried in the bed slide around too much.
I have the spray liner but also just got the bed mat for comfort for the dogs, my knees, and the kids when they hop around in it. I didn't use the provided Velcro and am still waiting for the bed mat to settle and even out from the curl it has from shipping.