Puzzles in RPGs?
Okay, now Puzzles.
My preffered method is to not use 'real' puzzles. Like no "and all three pressure plates need to be stood on in scheduled and timed sequence while the handle is pulled and someone chants 'Ominous Rex Internum' three times into the speaking tube in room 43a"... because even if you drop all the clues in the world, the frustration level of the PCs not solving it can be crushing on both sides of the screen.
Unless that's the game you and yours enjoy. That's the kicker, if your Players enjoy trying to brute-force code break puzzles, and you enjoy it, then go for it. Run wild and free. I certainly enjoy it as a Player (I love codebreaking too), but my Players tend to not go for it as much.
Otherwise, I suggest using the mechanic presented in D&D 4e (which was probably stolen from elsewhere but that's the first tiem I saw it), to wit, make it a skill challenge of sorts. Like convert the mechanic style over to your game of choice clearly, but it's basically like this:
SYSTEMLESS 'FANTASY' EXAMPLE:
The PCs encounter an obelisk in the center of the room with several other doors leading out, all doors are closed and cannot be opened by normal means. If the doors are examined with powers, each door resonates with a different 'Power'. If the obelisk is examined with powers, the PCs will discover it emanates "Power Type" energy that different power users can manipulate (magic, divine, psionic, nature, cheese, elder, etc). If examined mundanely, 'skilled' examiners can tell the obelisk can be rotated to face each door and 'locked' into place. With the right skill rolls you give it away, that they need to face the door, use that type of energy, and the door will open. If rotated away, the portal shuts again.
Now the above example doesn't mean that is the only way through the doors. Maybe an Earth power user could tunnel through the door, or around it (or just use pickaxes). Or if the doors are actually "Portals" that open to different areas, someone with Space/Gate powers might be able to open them using Gate/Space powers.
And the above is just a crude example of how to make a Puzzle that is solvable by the Characters (by relying on Character abilities, skills, attributes, etc) when it might not be easily solvable by the Players.
And you don't have to wait for the PCs to engage, you can start feeding the Players information based on what the Characters can see, hear, etc, passively. Like a highly skilled trapspringer might immediately notice the obelisk isn't "solidly in the floor, it might be moveable somehow". This method can help to spur engagement in Players that seem reluctant or disengaged with the game/puzzle.
But if you want to go even more 'abstract', you can just call for skill rolls and then tell the Players how their Characters solve the riddle. For some groups this works well, some groups less so.