How often does Disney re-theme things? I honestly don't know the answer to this. I'm just curious from people who know a lot more Disney than I do.
I mean, Rock N Rollercoaster is still Aerosmith, even though it could very easily be updated. I guess Mr. Toad was "re imagined" into Pooh, Aliens is a rethemed Mater clone, RSR a rethemed Test Track. TOT at DCA was rethemed but only because the Twilight Zone arrangement was running out.
It's a tricky question. I don't consider Mr. Toad going to Pooh a re-theme as much as a complete replacement.
With that in mind:
Mr. Toad / Winnie the Pooh
20,000 Leagues / Seven Dwarfs Mine Train & Little Mermaid
If You Had Wings / If You Could Fly / Dreamflight / Take Flight / Buzz Lightyear SRS
Mission to Mars / Stitch Encounter
Mickey Mouse Revue / Magic Journeys / Lion King show / PhilharMagic
Epcot:
Horizons / Mission: Space
Journey into Imagination / Journey into YOUR Imagination / Journey into Imagination with Figment
Universe of Energy / Ellen's Energy Adventure / Guardians
World of Motion / Test Track 1.0 / Test Track 2.0
The Living Seas / The Seas with Nemo and Friends
Magic Journeys / Captain EO / Honey I shrunk the Audience / Captain EO again / Pixar Shorts
Maelstrom / Frozen
Kitchen Kabaret / Food Rocks / Soarin'
Wonders of Life / Festival Center / Play Pavilion
DHS
Lights Motors Action and Backstage Tour / SW:GE
Star Tours 1.0 / Star Tours 2.0
Great Movie Ride / Mickey and Minnie's Runaway Railway
DAK
Countdown to Extinction / Dinosaur
Camp Minnie Mickey / Pandora
..probably some I'm missing