DT's instrumental sections are probably my favorite thing about the band... There are so many so I'll just have to list standouts from the discography
Instrumental Sections and their lengths:
Images And Words:Metropolis Pt.1 - 4:18 - 8:15 (4:01)
Learning To Live - 4:45 - 9:34 (4:49)
Metropolis Pt 2 SFAM:Fatal Tragedy - 3:50 - 6:50 (3:00)
Beyond This Life - 5:55 - 10:04 (4:09)
SDOIT:This Glass Prison - 9:41 - 12:52 (3:11)
Blind Faith - 4:59 - 8:23 (3:24)
The Great Debate - 9:27 - 13:45 (4:18)
literally every little instrumental section after each SDOIT disc 2 part is pretty great
Train Of Thought:Honor Thy Father - 5:02 - 8:44 (3:42)
In The Name Of God - 7:34 - 11:00 (3:26)
Systematic Chaos:The Ministry Of Lost Souls - 6:34 - 11:19 (4:45)
ITPOE Pt. 2 - 9:17 - 14:35 (5:18) THE RECKONINNGGGGNNSG
Black Clouds & Silver Linings:A Nightmare To Remember - 8:34 - 13:18 (4:44) minus the portnoy part
The Count Of Tuscany - 0:00 - 4:22 (4:22)
ADTOE:Lost Not Forgotten - 6:16 - 9:03 - (2:47)
Bridges In The Sky -7:14 - 8:57 - (1:43)
Outcry - 4:43 - 9:06 - (4:23)
Breaking All Illusions - 5:00 - 10:35 - (5:35) Also the longest DT inst. section, besides intros and instrumental songs. Edit: and besides TCOT
There aren't really many staple (as in long) DT instrumental sections in DT12, but ones that stand out to me are:
TEI 4:16 - 5:38 (1:22)
BTV 4:45 - 5:54 (1:09)
STR 3:44 - 4:35 (0:41)
IT 12:19 - 15:52 (3:33)
If I really had to narrow it down though, my tops would probably be Metropolis, LTL, BAI, The Glass Prison, and Beyond This Life