I've wanted to do the same thing and have been looking around for some time. The three options I've found:
BassTube, various brands: I think these kinda suck.
MTX ThunderForm: Come loaded with a 10" sub and a fairly decent amp. Tuned and ported box is contoured to fit against the right wall of the trunk. Doesn't really fit anywhere else. Inputs depend on the amp. Also comes as an empty box or with sub only. Not as many internet sites sell these. Usually costs more than the other two. Box with sub is around $200 new on Ebay.
Infinity Basslink or Basslink X: Basically a rectangular box with an powered 10" sub on one side and a passive 10" speaker, or radiator, on the opposite. Includes 200 watt built-in amp. Can be found on Ebay new in the box for less than $200. Elsewhere on the net for $220 and up (X model). The X model has a cooler looking clear chassis. Available with a wired remote volume control to mount under or around the dash. Box can be mounted upright or flat. Has line level and speaker inputs. Probably the best value but is not upgradeable like the MTX.
I'd also recommend a single 10/12 over a powered sub. Phoenix Gold is discontinuing their Titanium series: http://www.cbrstereo.com/index.asp?PageAction=VIEWPROD&ProdID=500 and one of these will perform great in a small sealed box. It all depends on what you want to spend, though. Don't just take everybody's word on which speakers suck or what sounds best. My advice for you is to go to some stereo shops, and demo a lot of different subs, and find what you like and go with it.
Some other recommendations, if you don't want to go with a single10/12, are a couple of Resonant Engineering RE8's, or a pair of Tang-Band 8's. They're meant for small ported boxes tuned fairly low, and they're not too expensive, so it might be something else to look at.