I love puzzles that come from information gathering rather than inventory items.
I love the computer work in both GABRIEL Knight 2 AND 3

I just remembered a couple of puzzles I dislike
timed puzzles, and puzzles based on memory, you push one , then two then three in a row, I make to 7 and am losing it, before I need the 8th to solve, HATE those kind.. think there was one of these in Whispered world. or maybe it was another game,

I like the way tomer described the puzzles, I like the ones, that are part of the whole plot.
I like to have a notebook, and work out the plot points, that lead me to solutions, but as I sit here cant think of specific puzzles, maybe like the ones in Alida, and GK.

Edited to add, I agree Tomer, I want to use Walkthroughs less, I think it can be a habit, when it is frustrating, to grab one, I want to also try and use it less, as solving things is the most fun in the game, I play for the puzzles first, then the story..
so I am doing myself a disservice if I use a walkthrough to soon.