My list would be very, very similar to Kev's.
Upon further review, I think this might have been more interesting to do, but not counting any DT CDs. In other words, your favorite 10 albums Portnoy plays on not counting any DT release.
1. Transatlantic - SMPTe
2. Transatlantic - Bridge Across Forever
3. Transatlantic - The Whirlwind
4. Neal Morse - Testimony Two
5. Liquid Tension Experiment - Volume 1
6. Liquid Tension Experiment - Volume 2
7. Neal Morse - ?
8. Neal Morse - One
9. OSI - Office of Strategic Influence
10. Neal Morse - Testimony
It is still waaaaaaaaaaaaaaay too early to accurately judge and rank the Flying Colors record.