Mesa Boogie Mark III Long Head (Reverb link).
The above shots (top, 12-3-14 TAB at 930 Club; bottom 10-29-14 Phish in SF) show the Mark III amps. The Mark III long head has been with Trey since the 80s and has appeared in various configurations, including oftentimes hidden behind the cabs and rack or standing on its side next to one of the cabs. The Mark III is a one-hundred watt amplifier with a half-power switch that shuts off 2 of the 4 6L6 tubes and runs it at 60 watts. The Mark III was also available in Mesa’s patented “Simul-Class” format, which would run at 75 watts or 15 watts. I’m not sure if Trey’s amps were Simul-Class.
The Mark III is a 3-channel amplifier, with a “Rhythm” Channel (aimed at mimicking Blackface Fender), a “Rhythm 2” Channel (light crunch/overdriven purr available), and a “Lead” Channel (searing leads available; think Metallica). It has onboard reverb and EQ. The long head is visually distinguished from other Mark III heads by:
(1) the fourth switch on the front panel. Other Mark III’s only have 3 switches: EQ, Power, Standby. The fourth is the half-power switch.
(2) the 8th knob on the front panel (it controls the reverb; this knob is on the back of other Mark IIIs).
Trey has said he purchased the original Mark III in 1985 or ’86. The dual-Mark III setup has been around for quite some time, as you can see from the shot below, from 12-3-94 (also, check out the 2×12’s):
Above, you can see a Boss FS-5U style footswitch labeled “BOOGIE LEAD CH,” indicating that, in addition to the gain stages in his two TS-9 pedals and the Compressor, Trey is also at least occasionally engaging (at least some of) the monster gain built in to the Mark III.
Trey's Guitar Rig 