Mostly from the top of my head:
Nine Inch Nails:
Closer To God, Closer (Thrust remix), the BYIT version, and Closer (Deviation) to the album version.
The piano version of Hurt
At least half of the songs on AATCHB, with special mention going to The Day The World Went Away
The BYIT versions of The Line Begins To Blur, Burn, The Big Come Down, and Only
Only (Richard X remix)
Zero-Sum (Stephen Morris and Gillian Gilbert remix) by a hair over the album version.
Find My Way (Oneohtrix Point Never remix)
Everything (Autolux remix)
The Wretched (Things Falling Apart and AATCHB versions)
Complications Of The Flesh, to both Complication and especially The New Flesh
The Day The World Went Away (Still)
Pretty much any live version of March Of The Pigs
Opeth:
The Roundhouse Tapes versions of Under The Weeping Moon, Bleak, Face Of Melinda, and Demon Of The Fall
The Royal Albert Hall versions of Forest Of October and Hope Leaves
Pink Floyd:
The following live recordings:
Plus the Pompeii versions of A Saucerful Of Secrets, One Of These Days, and Set The Controls For The Heart Of The Sun
Porcupine Tree:
The Sky Moves Sideways (34-minute alternate version)
Shesmovedon (2004 re-recording)
Synesthesia (Up The Downstair reissue version)
Even Less (full version)
There are probably some others, but, again, those were mostly from the top of my head.