For me, it's definitely SDOIT, 8VM, and SFAM, in that order. After that, I have a hard time sticking to an order of how I like the albums.
HEY EVERYONE WHATS YOUR 12 FAVOURITE DREAM THEATER ALBUMS AND ONE EP ?
You asked, although I won't include an EP.
At this very moment:
SDOIT
8VM
SFAM
DT12
I&W
Awake
TOT
ADTOE
SC
FII
BC&SL
WDADRU