For me, the last great album from the Portnoy era was Black Clouds and Silver Linings.
As for Octavarium, it's a pretty good album overall. I'm not the biggest fan of These Walls, I Walk Beside You and Never Enough, but I still enjoy listening to them when I listen to the album as a whole.
Also, The Root of All Evil and Sacrificed Sons are probably amongst my favorite Dream Theater songs ever.