Trey Anastasio has played the following guitars in this order, and still plays those with asterisks:

Pearl-white solid-body Ibanez
Time Guitars
Europe acoustic
Original blonde (1987) *
Padauk blonde (1990)
Koa hollowbody (1996) *
Wentzell acoustic *

Trey uses a midi-switchable rig with multiple loop paths. Trey uses Schaller pickups. Trey uses two Ibanez Tube Screamers, the classic TS-9 model. He has used a Bradshaw 3-channel preamp with old RCA tubes.

There is much more information available, as well as conflicting reports of what rigs Trey Anastasio uses at the link.
Source(s):
http://www.phish.net/faq/guitar.html

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