Bridges in the Sky, The Enemy Inside, Illumination Theory, Our New World, Barstool Warrior, S2N, At Wit's End and Pale Blue Dot I'd say are (or have the potential to become) MM era DT classics as well.
At Wits End and Breaking all Illusions would be the only classics of the mangini era. I don’t even looooove Breaking all Illusions as I think the vocal melodies are underwhelming but I will concede it as a classic.
Enemy inside is one of my least favorite Dream Theater songs, illumination theory is controversial and far from a classic, pale blue dot the same, S2N is a poor mans version of a SDOIT song.
I think our new world and barstool warrior are widely considered enjoyable but would you really put them up against metropolis, change of seasons, learning to live, spirit carries on, octavarium, take the time, trial of tears, fatal tragedy, SDOIT, etc.....?