Chris's setup

The setup Chris has been using since the recording of Absolution, and during all the Absolution tour is MIDI based.
This means he is able to control all his pedals with a single MIDI pedalboard and an expression pedal. There are two different pedalboards:

Pedalboard #1 (on stage)
This is the on stage pedalboard, it is very simple, it consists of the MIDI control and the expression pedal,.

Rocktron All Access
Korg Rack Mounted Tuner
Roland PK-5 Dynamis Foot Pedal

Pedalboard #2 (off stage)
The off stage pedalboard features a second Rocktron All Access and single effect pedals.

Rocktron All Access
Electro-Harmonix Big Muff
Akai Deep Impact
Human Gear Animato Distortion
Digitech Bass Synth Wah
Boss OC-2 Octave
Boss DD-3 Delay
Boss OD-2 Turbo Overdrive
Line6 Bass POD Pro

Here's a picture of the Rocktron All Access pedalboard... during Muse gigs, there are at least 4 or 5 running simultaneously... Chris and Matt have one, and so do their music technicians. This is a stand-alone foot controller, which can be customized in any way. Supports MIDIs and can be set in three operating modes: bank, song, and remote.

Korg Rack Tuner... Chris has one on stage, right behind the All Access... Matthew Bellamy has one, too.

And this is the Roland PK-5 Dynamic Foot Pedal... Has MIDI functions, and Chris uses it as an expression pedal for his effects. It has lots of effects, but I think Chris prefers using his single-effect pedals (placed in the FX loop of his amp).