I'm looking for resources for designing complex challenges – something that's not quite a puzzle and not quite a trap, but somewhere in between. There are tons of resources for really complex or off-the-wall deathtraps (such as this thread), but, while good, they're mostly let's-kill-some-adventurers traps.
The kind of puzzle-trap I'm looking for was created by the builder not to deter or kill adventurers, but to test their mettle – both physically and mentally. Failure to solve one won't necessarily result in getting crushed by a boulder or impaled on spikes – but if the players can't figure it out, the dragon or loremaster who built it might think they're not worth dealing with. Some might require skill checks or combat, but others won't. They aren't pure riddles, where "A box with no hinges, key or lid, but golden treasure inside is hid" is written on a door, and the players must answer "an egg" for the door to open. They can incorporate riddles, perhaps, but old-fashioned riddles are often known by the players and new ones often don't make sense in many RPG settings. And they aren't simple traps that the rogue can disable using a Thievery check or two.
The ur-example is the set of puzzle-traps in Indiana Jones and the Last Crusade, where Indy has to use his brains as much as his reflexes. Tower of God is another story that uses many of the types of puzzles I'm looking for.
Additional clarification: I want to avoid puzzles that depend entirely on the characters noticing things. In general, players assume that if they make a perception check or otherwise say "I look around, what do I see?", the GM will tell them everything of relevance (depending on the roll). If the GM simply tells the players they see the relevant thing at this point, the puzzle is over. If they don't tell, then the players will feel cheated – and will likely slow further adventures to a crawl as they meticulously describe every single thing they want to look at, from every angle. This can be a good trick when used sparingly and correctly (such as when the important item is tossed in the middle of a long list of description), but in general does not make for fun adventuring.
My group plays D&D4e, but I don't believe this is a setting-specific question. This kind of puzzle can – and should – be equally effective in WoD, Fate, or most other systems, since it's not mechanics that determine the outcome, but the players' ingenuity and creativity.
Where can I find resources to help me design this kind of puzzle-trap?
I highly recommend the fourthcore alphabet.
It is a series of tables with random base types and special properties yielding thousands of combinations. The two relevant sections are "T is for Traps" and "P is for Puzzles".
There's also a wealth of other information in there that could be used as inspiration for puzzles. I've drawn countless ideas from this resource.
Here's a sample puzzle I randomly generated in 30 seconds using the tables contained in the document: