I've been running two rigs for a while now and absolutely love it. I have a big board with lots of effects and use two Aguilar GS412's. I have a Sunn 1200s driving my 'bassy' rig and a 100w valve amp (changes round a bit at the moment) running my 'fx' rig. I split the signal at the start of the pedal board and have bassy distortions, fuzzes and octave down fx going into the Sunn and any quirky, noisy fx (wahs, ringmods, phasers reverbs, delays, synths etc) as well as an octave up running into the valve amp.
This way I have a big solid state amp delivering crushing low end with lots of meaty headroom and the breakup of a valve amp at full tilt at the same time. Awesome.
I think that having different fx (particularly if some are a bit 'out there') into separate amps creates an amazing array of textures and really works the kind of stuff I play.