Few days late here, but I agree completely with TAC regarding Hollow Years, and Beyond This Life - I really have to be in the mood for that improv section
Others I'll throw out
Octavarium - other than the extended intro, everything about this is better from RCMH
Six Degrees of Inner Turbulence - the orchestra makes is monumentally better.
Closer to the Heart - Different Stages version. Dat outro
Avantasia - The Scarecrow. Jorn gives one of the best vocal performances in prog metal. Ever.
Heart - The Voice (from Rock This House!)
Page/Plant - Four Sticks. I almost considered listing Kashmir
Evergrey - When the Walls go Down
Nightwish - anything Floor did from Annette's two albums
Star One - Intergalactic Space Crusaders. The chemistry between Allen and Wilson is amazing.
Triumph - Hold On... a little folk song you might remember. Making it pure acoustic is a great arrangement.
Entire Albums:
Operation:Livecrime
Mercy Falls - if only for the elimination of the cringy spoken parts
And some obvious classics
Freebird
With A Little Help From My Friends (Joe Cocker's version)
Do You Feel Like We Do
Alice's Restaurant (although, was there a "studio" version?)
Boom Boom (Out go the Lights)
Rubber Biscuit