A complete list of gear is almost impossible to create because it changes all the time.
John Petrucci currently uses Music Man guitars – and several different types. He has two distinct models: The JP model and the Majesty model.
In addition to this, Petrucci primarily uses the Mesa Boogie Mark V amplifier.
You can find a list (albeit a bit outdated) on http://www.johnpetrucci.com/gear.htm
Mike Mangini largely uses Pearl drums and Remo heads. The complete setup changes from album to album and tour to tour, but you can find a list of his gear here: http://www.mikemangini.com/gear/
Jordan Rudess is perhaps the most experimental in the band. He’s used so many different instruments in creating the sounds for the albums that it’s impossible to keep up. Examples include the Haken Continuum, the Roli Seaboard, several different iPad apps (many of which are co-created by Jordan in his company Wizdom music).
The current main synth Jordan uses is the Korg Kronos. He uses a Steinway Piano for piano recordings. You can find a list of gear he’s been using (albeit a bit out of date) here: http://www.jordanrudess.com/gear/
John Myung currently uses a Music-man Bongo bass: http://www.music-man.com/instruments/basses/bongo-6.html