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That's hard. I haven't heard all their albums anyway. But out of the material that I have, the one that sticks out for me is "Honor Thy Father," one of Mike Portnoy compositions on Train Of Thought. The instrumentals are awesome, seriously, it's one of their heaviest songs, it has some memorable riffs and amazing drumming, but the vocals don't fit with DT's style at all; LaBrie raps through most of the song.
I'm guessing it was Portnoy's idea, as he's the only member of the band that likes rap, that I know of. Bad idea, Mikey.