I'm a fan of the long-tube nitrate reactor design. Basically get a length of coild air-hose commonly used in construction and machine shops for lower pressure compressed air. Put the coil sealed in an appropriately sized PVC tube with one end coming out the top, and the other open inside the PVC. Fill the PVC with bioballs and drill an outlet into the top of the tube. Then you pump water very slowly into the air-hose, it takes a long long time to traverse down the tube. Along the tube, aerobic bacteria will grow to process ammonia/nitrite. These bacteria will remove O2 from the water inside the air-hose. Then eventually O2-free water leaves the end of the air hose and enters the chamber full of bioballs. There, anaerobic bacteria that process nitrates will grow and gobble them up, water eventually trickles out the top fitting and returns to the tank.
Search for "Nitrate Reactor" at about.com, they have a good guide for building one.