I've got a 2001 Wrangler (60th Anniversary) which came with the OEM sub. It's nice for the stock system but you would destroy the paper cone woofer with any decent amp.

I talked to a local car stereo place and they suggested replacing it with either the JL Audio 6" sub or modifying the internal sub box to fit an 8" woofer. I went the 8" woofer route and installed a used Kicker solobaric 8. The problem is that you can't find the round solobarics anymore, I got mine on ebay. Other speakers will certainly fit the bill but the enclosure size is small, only 0.3 cubic feet.

Check around the internet for other options for the jeep to see what other people have done. Some people have put free-air 10" subs in the center console but you need a big amp to drive them and keep them under control.