Um... DUH...
Here's my "gotcha!" list:
The Spirit Carries On (MUCH more so live sometimes)
Losing Time (this was more the first time I heard it, though)
The Answer Lies Within
Sacrificed Sons (It's hard for me to listen to this one, especially on 9/11 - I'm getting the feels just thinking about it.)
Octavarium (specifically Razor's Edge)
Repentance (rare, though - and it's during the long outro)
The Ministry of Lost Souls (the middle section kills the grandiose emotions though - IMO)
The Best of Times (My grandfather had passed away in September of 2008, and hearing the violin intro got me. I'm glad that I was able to thank MP for that song and tell him the story of how I connected the song to my Granddad.)
Far From Heaven
Breaking All Illusions (especially live - I'm a BIG ball of feels during the whole song)
Beneath the Surface
Illumination Theory ("To really feel the joy in life... " Man, I'm getting misty...
)