There were quite a few movies Roger Ebert liked that stunned Gene Siskel, but what about the other way around?
The only ones I can think of:
Rocky IV (1985)
Lambada (1990)
Career Opportunities (1991)
Any more?
Die Hard
shareThe time he slipped it up Roger’s butt. That was surprising.
shareCarnosaur
Brain Candy
Starship Troopers
Batman
Batman Returns
Batman Forever
Spaceballs
Adventures in Babysitting
A Very Brady Sequel
Remember, the current site that's archiving their old shows is https://siskelebert.org/
Probably the most surprising thumbs-up by Siskel was the infamous "The Island of Dr. Moreau" (1996), which you can watch here: https://www.youtube.com/watch?v=YYX3KIi6ZJ4. Ebert gave it thumbs-down. This showed that Gene was willing to break from the snobbish critical consensus if he honestly enjoyed a movie, even if he'd be ridiculed for his opinion.
"Carnosaur" is another example in which he surprisingly gave the flick a thumbs-up and Ebert a thumbs-down.
Also:
Fun House (1981)
From Beyond (1986)
Parents (1989)
Out For Justice (1991)
Beethoven (1992)
Straight Talk (1992)
Brain Candy (1992)
Eddie (1996)
Larger Than Life (1996)
The Island of Dr. Moreau (1996)
Fierce Creatures (1997)
I heard Siskel liked Halloween III (1982) as well - I wonder if it's actually true?