There are tons of great brands around, but it depends on your budget. In the $200-ish area, the most sub you can buy is either going to be a BIC or a Cadence. You'll find that in the sub-$1000 price class for things, spending an extra $100-200 will yield some big differences. After that, it takes more money to really get a difference.
If you're looking to do some sweet upgrades on a budget, I'll have to plug BIC speakers yet again. For $125/pr shipped, I don't think you can buy better bookshelf speakers. They play clean, clear, and LOUD. Great bass too, especially for the size of the speaker. I can guarantee that a set of these and either that BIC sub I posted or the slightly more expensive Cadence sub would be an amazing improvement to your current system. And it would give you a chance to use those beautiful racks! I'd say you can put together a 5.1 system with speakers, subwoofer, receiver, and DVD player for under $1000, cables included.