I say that the sub box style depends on what you're going for. If you're aiming for overall listening enjoyment, do a sealed box. If you want to set off car alarms and rattle windows, do a ported box.
Grimm is dead right about matching the volume of the enclosure to the mfg recommended size. You can cheat a little bit by using polyfill (it slows the sound wave down inside). He's also got a good point about cabin gain. I used to have a 12" JL in a properly sized sealed box in my XJ... It wasn't quiet.
I love a good strong response at 20Hz or so. Not only can I hear it (I've been tested and I have really, really good hearing), but you feel it. The problem is finding songs with clean signal that low in frequency. Most head units will output 5 Hz to 20kHz... The trick is getting a good response across the range.
As far as materials... well, how stealth are you looking to go? If you want to sink it into a cubby in the side of the xj, make it out of fiberglass. If you just want a box, make it out of 3/4" thick MDF. MDF has very good sound characteristics because there are no voids in it. It also happens to be cheap as compared to Russian birch plywood.
Positioning in the vehicle will affect how it hits. My 12" was pointed at the back hatch and that seemed to hit really well. I never experimented with any other options in my XJ.
Here's what I recently installed in my DD... Note that it's a hatchback - the interior is one open cabin just like the XJ. I've still got some kinks to iron out in it, but I like it a lot so far. Having the sub pointed up at the ceiling seems to be working well.
So, specifically directed to the OP: How crazy do you want to get with this? If you put in a big boomin' sub you're going to want to upgrade the rest of your system. I originally installed only a sub and kept the stock speakers. Guess what? It sounded like crap. So, decide how you want it to sound and how much you want to spend. I'll do my best to try to help you go from there.
Hope that helped.