Couple things -
There are HD Tracks for all the RoadRunner albums - Systematic Chaos, Black Clouds, ADTOE, and 12. Plus, Breaking the Fourth Wall. These are by far the best versions of those albums (not sure whether it's the same as the vinyl or what).
For vinyls - Music on Vinyl look the best, but they don't sound the best. Brookvale sound the best. I wouldn't buy any more MoV's.
For Images, Awake, and FII - the CD's sound absolutely great. The albums were expertly produced and mastered.
Same is probably true for Scenes and SDOIT, even if they weren't done quite as well.
There are no great sounding versions of ToT or Octavarium, aside from what's on the CD (as far as I know).