OK, I’ll use my IF top 50 nominees as a list that isn’t directly influenced by this question. Total spoilers, obviously.
Photopia:
Well, it’s the maze, which actually probably counts as a puzzle.
Galatea:
I think it might be the time Aphrodite came in and killed her? Not a puzzle. Of course the game is largely puzzleless.
Spider and Web:
You think I’m going to say That Puzzle, but it’s actually a tie between That Puzzle and the introduction.
Best of Three:
Grant’s tea order, definitely. Not only is this not a puzzle – it’s a puzzleless game – it’s not even interactive, really. It’s basically part of a cutscene.
Shrapnel:
Ah, hell, I don’t even know. The first time you restart, maybe? Anyway, not a puzzle, and the game is pretty much puzzleless.
The Firebird:
Hm. I think maybe it’s part of the assault on the mountain when everyone else shows up? I’d call this not a puzzle.
Blue Chairs:
It might be the various people frozen in the labyrinth, or maybe the very ending – not the puzzle at the very end, which I didn’t like and had to use the walkthrough, but the end. Anyway, it’s not a puzzle. There are a couple puzzles I remember, but they’re not it.
The Act of Misdirection:
End of Act I for moment; maybe all of Act I for scene. The end of Act I isn’t a puzzle, and I’m going to score the whole thing not a puzzle, because that’s not what I like about it.
Rover’s Day Out:
For moment, it’s probably the commentary about why they didn’t implement the plate. That wouldn’t count as a scene, though. For the scene, it’s probably going through the routine the third time, which I guess counts as a puzzle – I think it’s roughly what got nominated for the XYZZY. Half a point.
The Baron:
A conversation with the gargoyle about free will. Not a puzzle, but the game probably counts as puzzleless.
A New Life:
Hm. I might say figuring out a way to get objects across the forcefield; that’s definitely what I’d say if asked what thing I liked best about it, that and figuring out where a certain hole went not that I could ever do anything with the hole. But I think I’d only say that if prompted that moment means puzzle, and it’s definitely not a scene. It’s what I’d say if asked what the single best thing I like was. If I’m talking scenes, and maybe moments, it’s the bit where one move takes you halfway across the map with a few pauses for space. Half a point, partly because I’m cheaping out by not awarding half a point to Act of Misidirection.
Pick Up The Phone Booth And Aisle:
Northeast. Not a puzzle but… no, the hell with it, I’m going to be a hardass and count this is not puzzleless. If Photopia has puzzles so does this, specifically how do you win?
OK, I count that as one and three-halves out of twelve; but four of the games were puzzleless, so it might be one and three-halves about of eight possibilities. On the other hand that list didn’t run to games I like for their puzzles; if I were drawing up a list of best individual puzzles only three of them would make the list.