Interesting... most games in my top ten have already been mentioned, although good puzzles are definitely not my only criterium.
Plus
Bad Mojo for its creative cockroach puzzles: no inventory, no hands. I wish there were more games featuring weird creatures with unique possibilities. I was a disappointed that alien Squish with his 6 arms - 4 ordinary ones, 1 retractable and 1 inflatable
- is just an NPC in Callahan's Crosstime Saloon.
The lovely, whacky, humorous puzzles in
Zork Grand Inquisitor.
The natural, well-integrated "puzzles" and problems in the
Last Express.