From what I know, mixolydian and dorian get used a lot. Here are a few lessons that I typed up from a magazine on Trey's style in Phish.
(Slightly outdated) Electronic and classical compositions by m'self: Check 'em out
hey thanks man that magazine article was alot of help. i just remembered that i also have a bunch of lessons by trey in my latest guitar player magazine.
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all the modes of the major scale
modes of harmonic minor
melodic minor
minor and major pentatonic
major and minor hexatonic

those are the ones that i find common, but any scales can be used to jam

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