Um... all of them? Hahaha.

I guess, if I were to pick a single song from each album that showcases probably the best guitar work, it would have to be.. umm....

Images and Words: Under a Glass Moon
Awake: Innocence Faded
Falling Into Infinity: Raise the Knife (not actually on the album, but it was supposed to be, and is better than anything that did make the cut. Refer to the live version from the Score DVD to have your mind melted)
Scenes From a Memory: Fatal Tragedy
Six Degrees: a hard one.... Either The Great Debate or The Test That Stumped Them All
Train of Thought: In the Name of God would have to be my favorite, just because of the mad riffage. But that whole album is covered in great guitar work, save for Vacant
Octavarium: The opening riff to These Walls might be my favorite guitar moment, but I think Octavarium (the song) would definitely be the best example of Petrucci killing it.
Systematic Chaos: In the Presence of Enemies Pt 2. Dat solo.... omg....
Black Clouds & Silver Linings: The cover of Rainbow's "Stargazer" from the collector's edition bonus CD
Dramatic Turn of Events: Breaking all Illusions
Dat new album: The Looking Glass

But seriously though, asking to list the "guitar-dominated tunes" from Dream Theater is a pretty damn vague request.