The only truly clueless "what the...?" comment I'd ever really heard was from my own partner. The first time I took him to WDW and we went to Epcot, we hopped on Spaceship Earth. He looked a little confused when we had to sit in a moving vehicle. Then when we went up and up and up past all the great vignettes, he looked even more puzzled, craning his neck about, looking high and low.
As the attraction came to an end, he kept oggling and muttering. If we were a cartoon, he'd have had a permanent question mark posted above his noggin. I asked him what he was looking for.
"The countries."
"What countries? That was Spaceship Earth."
"Then where are the countries?"
"Outside... wait a minute... you mean..."
Practically scratching his head, he asked, "Outside? Why are they outside?"
This went on for a minute as we strolled through the ATT Global Neighborhood displays. His confusion led to my confusion. And so it went.
We went on to the rest of Future World and enjoyed ourselves. As we moved in to the World Showcase, I saw Joe's cheeks start burning beat red and he wouldn't look me in the eye. So I had to ask.
"Now what?"
Very reluctantly, he muttered, "Nothing."
"What? Tell me."
After a couple minutes prodding, he admitted that prior to this trip, he had always thought all of Epcot was inside the "big golf ball thing", with tables set up with little signs stating what country they represent. He never could understand why anyone would ever want to spend money or time visiting something like that.
"You mean to tell me that after MGM and Magic Kingdom, you'd think that Disney would do something like THAT?"
His response? "Shut up."
By the way, Epcot has grown to become his absolute #1 favorite park. And yes, I still get on his case whenever we visit. "Hey! Let's go to the big golf ball thing and check out the tables!"
Always zinging eachother. 
It is only funny when *I* make fun of *other* people!
