Metropolis is unanimous and it makes sense
Easily Metropolis, because it has the vocals as well. James is an integral part of DT's "signature sound". Otherwise, we have the exact same reaction to Ytse Jam. I hear the words "Dream Theater", and bam, dun dun duuun, dun dun duuun *queue more DUNs*.
Someone who shares the Ytse Jam angle with me!
As I said in my first post for me it's either Ytse Jam or Metropolis, actually it's both. Ytse Jam is song I think could have fitted in any other Dream Theater album, it was their first instrumental and to me their first "That's what we'll be about" statement, an angle that remained solid through out their career; instruments giving the floor to one another back and forth, little wankery here and there and most of all musicianship and instrument command that never declined. It's all about taste and none of this makes Ytse Jam a better song but it's undoubtedly one of the iconic Dream Theater songs and a sure contender for signature song.
Well, initially it was PMU but Metro is probably more representative overall.
That's the second part of my OP question, to most of us fans it's Metropolis but to casual DT listeners from rock and metal fans I think it remains Pull Me Under.