Actually, the single most improbable element of the Mount Rushmore sequence, I found, was the idea that there was a private home and airstrip on top of Mount Rushmore.
Manos, the Hands of Fate runs away quickly
I’d like to see Ghostbusters get cleaned up in a few places where the effects are less than completely convincing. I’m thinking specifically about portions of the battle with Zuul and some of the Slimer sequences.
I’m glad you said that, Forbidden Planet in particular stands out as a film whose effects were great without the need for any post 1970s film technology.
But there were some bits in ST - TMP - CE that were supposedly an improvement over the original that just weren’t, the blocks that whipped up into place around the saucer section spring to mind.
I would like to see “Things to Come” or “Metropolis” redone with updated, but well written scripts (not will smith punching the robot and cracking a corny joke).
Now THAT would be cool!
How 'bout “Attack of the Killer Tomatoes” being redone with CGI?
Imagine all those tomatoes with evil faces! Running over all those bad actors and squishing them back to their day jobs?
Ketchup LIVES! 
If you’ll allow TV shows, I’ll say the original Twilight Zone. I just watched a few episodes recently for the first time in a long time. I’m not a special effects junkie, but the effects on the Twilight Zone are bad to the point of distraction. Even on classic episodes like the one with William Shatner seeing the gremlin on the airplane – that gremlin looks so bad it ruins the whole scene. And another episode where an airplane mysteriously goes back in time, the crew looks out the window and sees…a claymation dinosaur. I could only laugh.
They did that a couple years ago, with Forest Whitaker as the host. It didn’t completely suck, though it rushed to cancellation.
War of the Worlds!
Without Spielberg or Cruise… Well, maybe Spielberg could play Dr. Clayton Forrester
A few science fiction movies occur to me:
The Day The Earth Stood Still.
Metropolis
A Boy and His Dog
Flash Gordon
Logan’s Run (another pass at the script wouldn’t hurt, either.)
War Games
Westworld (with a silent inhumanly strong Clint Eastwood in the Yul Brynner role)
and finally,
I, Robot – with the Asimov series adapted by Harlan Ellison script, dammit.
Then who would play TV’s Frank?
Forbidden Planet