For self-created puzzles, I might go with working off a series of some sort (color, numerical, etc.) Scattered codes and keys can work well. I think it's important to integrate it into the particular situation then to just have an arbitrary puzzle (that is both annoying and smacks of the old adventure game trick of introducing puzzles just to keep the players from zipping through their $40 game too quickly).
I don't actually make a lot of use of puzzles. The most recent one was basically a combination lock requiring 3 particular symbols. The lock required the 7th symbol in 3 series. The players found the elements of the series in 6 particular chambers scattered across the land. Each had an element in the series and a 4th symbol in an archaic counting system that was the square of the order of the symbol set (so first set of symbols was with 1, second with 4, third with 9, etc.). That way they could find the symbols in an abitrary order and use the square series to order the other symbols.
One symbol series was graphical (a 5 pointed star with a tip that rotated 2 positions every step and a line that moved one per). The second was a simple alphabetic, 1 forward, 1 foward, 2 back and the third was another graphical series using the number of sides of an object (where 1 sided was a circle and 2 sided was a plus sign).
As it happened, the players cracked the code in minutes but the bulk of the puzzle was actually finding the chambers, acquiring the information without visiting some chambers, finding maps, stealing notes, subverting bodyguards, and dealing with a wizard trying to crack the code. So the fact that they could crack it quickly was not a big deal. You never know if the players will "get" it or spend a frustrating hour on the puzzle, steadily getting more annoyed.
The whole thing started when the wizard "paid them" to search for a certain chamber and get an unrelated and unimportant rubbing in that chamber that would only prove to the wizard that they had spent time in the chamber. In reality he knew where the chamber was but he also knew there was a powerful wraith in there that would go dormant after taking a life so he just wanted the party to take care of the wraith by killing it or providing a life to satiate the wraith. As it happened we were all new to 4E and my wraith turned out to be not as powerful as I thought: they killed it.
But it made an interesting villain that the party was royally pissed at. He showed up at times, sometimes in places where they couldn't kill him (at a court) other times by rumor or repute. They chose to pursue the puzzle as much to get back at the wizard as for the supposed loot.
Anyway, it's an example of a puzzle but one that they could have abandoned at any time (I don't like to make them mandatory) and it had a lot more to it than just the pure puzzle bit. There was more back story as to why the chamber was there as well.
Another puzzle I can remember was much longer ago and just a basic puzzle (i.e., no grand integration into the scenario). There was a grid of many different colors. The only safe path through it was to trace the colors of the rainbow.
Another puzzle wasn't key to solving anything but might have helped them progress faster: they were searching for god who they knew took the form of a dragon and had been "sleeping" for millenia. I made a 3D model of sleeping dragon -shaped island and used Bryce to animate a fly-around the island: the god had been covered with stone. That one didn't work. They didn't recognize it. Not sure if it was the lack of artistic merit of my attempt or just the difficulty the players had of imagining the situation.
One thing you can do is buy a book of puzzles and adapt them to your game...