I can't pick one, but my favourite MP songs to drum along to are:
Learning to Live - one his most challenging, considering there's very little formula to it. Lots of beat changes as well
The Great Debate - pure drumming ecstacy
Lines in the Sand - this is the funnest to drum to
Afterlife - A lot of Portnoy-isms that he stopped using can be found here
Another Won - Again, very little formula, and I think I have pretty much every single beat in this song memorized.
Finally Free - The ending
Metropolis - Another song I've have pretty much ingrained in my head. I've played along to this song probably 500 times by now. It never gets old.