There are many good reasons to buy pre-built, warranty, after sales support, ease of use and setup. However, there are some great reasons to build as well. You can get a bit more bang for your buck by building. It really boils down to what's most important to you, how much time and effort you want to put into it, and what your end goals are.
IMO, if this is for a home theatre setup I'd build, but I'm biased because that's the route I went and I think for $1000 you can build a sub that will at least equal the performance of the commercial options at that price range. However, I'll also be the first to say that this route isn't for everyone.
Car audio drivers can be very good, but we need a little more information to decisively say where this would fit in. Pesonally I like external amplifiers and would go with something like the Crest Pro Lite. It can power up to two subs and if you go with the 3.0, 5.0, or 7.0, will drive just about anything you can build to substantial levels.