Not sure if all of these are controversial, but lets go:
In the Presence of Enemies Part 1 is the best opener on any DT album (even though Systematic Chaos as a whole is one of their worst albums)
As much as I don't like the album, Constant Motion is actually not a bad song. It's actually my most listened to DT-song, and it has a pretty catchy chorus. Not saying it's the best or anything, but if DT wanted to make a Metallica-sounding single with it, they did a pretty good job IMO
Breaking All Illusions is the best +10 minute song since 6DOIT (yes, that means I hold it even higher than Octavarium)
If you chose to count it as one song, Six Degrees of Inner Turbulence is the best DT epic IMO
While the songs individually might not all be up among DT's best, the twelve step suite is actually one of the more interesting things they've done
Train of Thought is not as bad as the reputation it has gotten, and with the exception of ADTOE, it's the best album to have come out of DT's last 11 years
Falling Into Infinity is despite of label interference one of the better DT albums. I would rank it at nr5. It might have some lame attempts at writing radio hits, but there's also several really great tracks like "Lines in the Sand" and "Trial of Tears"
Disappear is the most emotional, and also the best DT song