I might have already put it somewhere here in December, but there have been changes...
1. Systematic Chaos
2. Six Degrees of Inner Turbulence
3. A Dramatic Turn of Events
4. Train of Thought
5. Octavarium
6. Black Clouds and Silver Linings
7. Scenes from a Memory
8. When Dream and Day Unite (realising how much Dominici reminds me of Geddy Lee helped me a lot with the appreciation)
9. Falling into Infinity
10. Dream Theater
11. A Change of Seasons
12. Awake
13. Images and Words (an "EP" with just Take the Time, Met 1 and Glass Moon would be probably in my top 5)
14. The Astonishing (I would rather not rate it at all, but...)
I'm pretty constant in my ranking, though ACOS has grown upon me a bit lately (though I'd still prefer it to be shortened to about 15 mins or so).