Besides the obvious benefits of his awesome technique and killer Beneteau guitars (I own 2 of his old ones, lucky me!) his setup is pretty basic. He uses a Mackie 1202 mixer, Boss ME-50 for a couple random effects (wah, distortion, chorus) and his main preamp is the K&K Quantum Blender. His standard pitch guitars typically have a K&K Trinity system (SBTs + internal mic) - his fanfret sunburst baritone has a Baggs I-beam and M1 combo.
Lately, he has been messing with a new instrument called the Frameworks guitar - he runs that through a Fishman Aura. Strange looking, but I've heard him get some pretty killer sounds from it in a live setting.
Here's a photo you'll find interesting that shows the settings on his preamp - click on the pic to make it bigger:
http://www.gobyfish.com/photos/Dan_Miner_photo.JPG
Let me know if you have any really specific questions and I'll relate them to him.