Best subwoofer?

I have 2 Rel Stadium III's, they sound great with HT, one front & one rear. I use them for LFE input only. I too use a Meridian G68/598 for my HT.
I purchased an Aereal Acoustics SW12 because I wanted more flexability, like high & low pass filters & an EQ for my 2 channel analog setup. It intergrated flawlessly with my front speakers. I will try it with my HT later after I get a second one.

Any REL sub!

SVS The very best for the money! SVS subs blow away any sub costing three times as much!

The best that I have heard are the Cabasse Saturn 55 Active Subwoofers which are hideously expensive. A 21" concave Cabasse woofer (built in their factory) in a 37" by 33" by 28" box with a 1200 watt amp, parametric EQ and low pass filter, capable of generating 135.5 db at 1 meter. 350# per side, massive and inert. I had used these in the past with a pair of Acapella Campanile speakers with mixed results (the bottom octave was fabulous but they never mated perfectly with the Campaniles. Two weeks ago, I set up a pair of Acapella Triolons in my system which use a horn loaded 12" woofer to cover the range from 170-700 hz rather than multiple 10" SEAS drivers in an acoustic suspension enclosure). For whatever reason, the mating is seamless with the subs crossed at 40 hz. Normally you do not realize that these are in the system, except for an increase in low level ambient information and air and a concommitant increase in the volume of the sound stage, particularly with respect to depth.
However, when low bass exists, the response can be awsome. Are these really the best subs? Who really knows? What I do know is that they are by quite a margin the best that I have heard when used properly in the right system.

The Legacy LF Extreme with Level, Freq, Blend and Phase controls makes for effortless integration and the 15in drivers let you into the basement for low bass and depth.