I always acknowledged Octavarium, but never really gave it enough respect until recently.  I passed it off as being too mainstream sounding, which on the surface it was.  It's not until you actually take the time (hurrdurr) to really listen to it that you start to understand how much more complex it is.  
And yes, These Walls was one of the first tracks on that album that made me take notice.  
Although, I gotta say, a lot of Dream Theater's latter day stuff didn't grab me at first.  Train of Thought, Octavarium and Systematic Chaos took a while for me.  So did Six Degrees (despite The Glass Prison being my favourite DT song).  

My absolute number 1 is still Awake though.  That to me is probably the most encompassing album, and the strongest in terms of songwriting and performances.  It was heavy, it was dark, but it was still melodic and it pushed their sound further outwards.  
Then it's Images & Words, and then Scenes From a Memory.