Best subwoofer for 2 channel Hi End system

Vandersteen 2WQ. Even better, a pair of Vandersteen 2WQs.

I totally agree with Swampwalker. The 2Wq is an excellent sub for music and with the "Q" adjustment, you can get it to integrate seemlessly with about any speaker.
A pair is better for several reasons. One, it loads the room better for smoother response and second, there is some information in the lower range that is channel dependent.
I personally have found that 2 enhances the soundstage width and depth over using 1 sub that sums the low frequency information.
Also, as a final thought, the 2Wq is driven at speaker level. This removes the responsibility from the preamp and also allows the sub to take on the general characteristics of the driving amplifier for better blending.
It is a well designed and executed sub.

Because I believe that even very low frequencies provide directional information, and because most subs are front firing, I've never accepted the "one-subwoofer-is-all-you-need" theory. And down-firing subs, although theoretically omnidirectional, always seemed to lack good transient response (which is very important to me since my mains are electrostats.)

Recently, I installed a single new Martin Logan Depth, for reasons which I explain in the comments to my system specs (under my ID "nsgarch") here on AgoN.