A lot of Metropolis Pt. 2: Scenes from a Memory is incredibly unsettling. It begins with a very calm hypnotist and then his patient relating information. All of the spoken word aspects are very monotone, but the singing sounds strangely upbeat and then the background noises start getting harder to ignore.
"Open your eyes, Nicholas." AHH! *THUD* *record scratch* *static*
Especially disturbing as the "Open your eyes" comes up earlier in the song: " * BANG* * SCREAM* "Open your eyes, Victoria." * BANG* ". The whole murder scene is incredibly creepy simply because it's related with sound rather than lyrics.
All of "Six Degrees of Inner Turbulence" can be Nightmare Fuel to anyone who has one of the disorders the songs are based on.
Don't cross the crooked step!
"In the Name of God", about the Branch Davidian religious cult and their siege in Waco, Texas in 1993. Especially the way James describes how innocent members of the cult dropped like flies during the standoff.
"Panic Attack" symbolizes its namesake pretty well, with its disjointed lyrics and chaotic music. If you're prone to panic attacks, you'll know that it's pretty accurate.
"The Dark Eternal Night". The lyrics are about a mummy coming back to life and summoning an undead army to take over the world. As if that wasn't bad enough, the music is extremely violent in its tempo changes and even has a very creepy honky-tonk piano section that always is enough to creep one out.
"In the Presence of Enemies: Part 2" begins with the sound of wind followed by a very creepy bass and piano part. James LaBrie's singing in this section also helps with making you feel uneasy.
Their cover of "Flick of the Wrist" by Queen on the special edition of Black Clouds & Silver Linings, specifically the way LaBrie sings the verses.
"The Enemy Inside" is already a disturbing enough song about PTSD. The video adds to that, with its frighteningly realistic depiction of a traumatized father unable to execute simple everyday tasks without worrying about being shot.