Nice thread! Here's my take, with some comments at the end:
1. Octavarium
2. A Mind Beside Itself
3. A Change of Seasons
4. SDOIT
5. ITPOE
6. FFH/BAI
7. The Count of Tuscany
8. The Ministry of Lost Souls
9. In the Name of God
10. A Nightmare to Remember
Probably because I was a fan of older prog rock before becoming a Dream Theater fan, I have a huge soft spot for Octavarium. SDOIT ranks a bit below the top simply because it's SOO long and gets a bit repetitive at that length. But still, it's good enough for #4.
FFH/BAI I have trouble integrating into 1 song. They don't feel "epic" to me, like a long song should. That being said, I LOVE those songs. Just not as "15+ minute" style songs.
TMOLS/ITNOG, same thing (but not as good as FFH/BAI). They both feel like 10-12 minute songs with filler added to puff them up. Good songs, but not epic.
The Count of Tuscany is probably better than I rated it, but that whole album left such a sour taste in my mouth that I never gave it much of a chance, much of that due to...
ANTR, which had so much potential until the growling vocals ripped the soul straight out of my body.
All IMO, of course.