The Shinteki series frequently will have non-puzzle challenges. For example, in Untamed teams had to put in order the distances between four pairs of orbs in a field. The lengths were each about 60' but differed by only an inch or two from each other. No amount of Braille or Morse decoding will help with this challenge, but I thought it was great because it was a "puzzle" to figure how to make these measurments. (Since then, my team now always carries a 200' measuring tape.)
Besides these challenges I also enjoy real puzzles that have been masked to appear as an ordinary object to the unexpected observer. Ie, a puzzle that's left out in the open but that no one not in the game suspects is actually encoding anything. These puzzles are admittedly very difficult to construct, because they often depend on the environment (ie, they need to blend in and possibly use features of the surroundings in the puzzle). For the McGuffin Game spongiform created a "newsletter" and map left at the Oyster Bay Regional Shoreline in the map box. Teams were told the next puzzle location was the Oyster Bay site but given no details. Clever teams who looked for the map (right at the entrance) would immediately notice puzzle-esque things in the newsletter -- a lot of numbers, and the map had dots with letters on the back. But what was brilliant about this puzzle, in my opinion, was that the document otherwise looked entirely plausible as an ordinary object. In fact we saw a few park visitors not part of the game pick up the map.
Some people are motivated by the puzzling aspect of these games, and I respect that. In a conversation a while back with onigame he said he'd get just as much fun out of solving all these puzzles in a conference room somewhere as driving around in a van finding clues in the field. For me, though, I get my thrills elsewhere. Unfortunately, because these puzzles are somewhat more challenging to create, I don't get many of them.
In the upcoming Hogwarts game I have high hopes. The puzzle for the application page was a great example of the type I liked. It's an eye chart, and to the unsuspecting observer that's all it is. Only in a game when you're on high puzzle alert would you suspect there's a message encoded in it. It's actually interesting -- in a conversation with some of my teammates earlier I was lamenting how I generally didn't like the puzzling style of the team who's putting on the Hogwarts game. I still think there's a subtle elegance that the puzzles sometimes lack, but realizing that their puzzles *do* often have this hidden-puzzle flavor to them has me more excited about the upcoming game again.