Another vote for ** Konstantine ** by Something Corporate. One of the most affecting songs I’ve heard in years.
I believe it’s available for free on mp3.com, if anyone’s interested.
Well some overlooked favorites of mine are:
“Spare Chaynge” & “Bear Melt” by Jefferson Airplane
the “Empire” suite from Paul Kantner & (the original) Jefferson Starship
“Saint Stephen/the Eleven” by the Grateful Dead (actually, both songs alone are over eight minutes apiece, but strung together on “Live/Dead” as one long suit.) as well as “Not Fade Away/Going Down the Road Feeling Bad.”
“Down by the River” by Neil Young
“Ball & Chain” by Janis Joplin
and “Tubular Bells” by (I think it’s) Michael Oldfield
Oops! Just remembered “disintegration” by the cure is over 8 minutes long. Since I voted for that as the best song ever in another thread, I can’t rightly contradict myself in this one.
“Third Eye” is my favorite song over 9 minutes. 
My God. Over 60 replies, and not one has mentioned Emerson Lake & Palmer? What’s wrong with you people??
Check it out:
“Karn Evil 9” (29:32)
“Tarkus” (20:31)
“Pictures at an Exhibition” (33:48)
“Take a Pebble” (12:37)
“The Endless Enigma” (10:34)
“Trilogy” (8:54)
“Fanfare for the Common Man” (9:38)
“Pirates” (13:20)
Also, to Jethro Tull, add “Heavy Horses” (8:57), “Minstrel in the Gallery” (8:09), “Dark Ages” (9:07), “Baker St. Muse” (16:40) and “Budapest” (10:00).
Many good Yes songs have already been mentioned, but I didn’t notice “Awaken” and “Machine Messiah” (too lazy to look up the times…)
A few more of my favorites that I didn’t mention in the OP:
First, a hearty second to casdave’s mention of “Autobahn” by Kraftwerk, a 22:41 masterpiece. That song is like aural Jelly Bellies to me. I hadn’t really meant to limit this thread specifically to rock music. That word just sort of came out when I was typing.
Tori Amos - “Yes, Anastasia” - 9:32
Tori Amos - “Datura” - 8:25
Rush - “The Camera Eye” - 10:58
Mother Love Bone - “Chloe Dancer/Crown of Thorns” - 8:19
The Cure - “Fascination Street (remix)” - 8:48, and I like it much better than the shorter original
Outlaws - “Green Grass and High Tides” - 9:47
Elton John - “Funeral For a Friend/Love Lies Bleeding” - 11:02
The Pogues - “The Band Played Waltzing Matilda” - 8:10
Tool - “Opiate” - 8:29
Here’s one that hasn’t been mentioned (and one probably not many people know of), Mogwai Fear Satan by Mogwai, which clocks in at about 16 minutes. Mmm, instrumental guitars…
Sonic Youth - The Diamond Sea
Slint - Washer
Can - Halleluwah
I was going to say one of these, but then I remembered…
Neutral Milk Hotel - Oh Comely
Here are a few more, in no particular order:
Roll Over Beethoven, ELO
Who Do You Love Suite, Quicksilver MS
Spoonful, Cream
Talking About Goose Creek, Goose Creek
Willie The Pimp, Frank Zappa
California, John Mayall
Low Spark of High Heeled Boys, Traffic
Fleetwood Mac with Peter Green had several over 8 minutes: Jenny Jenny, Green Manalishi, and Rattlesnake Shake
And IIRC, King Crimson’s, In The Court of the Crimson King, album had a lot of very good, long songs on it, and I’m sure some are over 8 mins.
Need to throw some Metallica in, so here goes:
Master of Puppets 8:36
The Call of Ktulu 8:55
The Outlaw Torn 9:48 (yes, I know Load sucks, but I like this song)
Fade to Black (Cunning Stunts version) 8:08
To Live is to Die 9:48
There’s five candidates right there. I pick Master.
-brianjedi
Oops, I meant to add something there about how those’re some great choices, but I accidentally hit submit. oops.
Starship Trooper.
I told her I wanted to make love to her badly. She said I would have to do better than that.