dungeon puzzle help

[Chaoticway]

So I'm running a 3.5 campaign that has been going over a year so far and starting to run a lil dry on creative ideas. Soon enough the party will be traveling to an ancient city to find a magic well that they can use to attain the location of the final boss's base. No one except a bunch of lizardmen and Naga have set foot in the city in thousands of years. The city is in disarray, buildings crumbled or taken back by the jungle. They know the well is in a building in the city, just not which building. Using a series of wisdom or intelligence checks they will be able to make some observations of the few buildings the well could be in. In effect, the whole city is a massive dungeon with a series of small dungeons within it. I've already made the 5 building maps. They all are relatively similar, one large central room, with few rooms surrounding the central chamber. Each of the smaller outside rooms I want to have some sort of puzzle or something they have to do in each room that unlocks the central chamber. The buildings are a manor house/castle, a barracks/detention center, a treasury/vault, an observatory, and an archive/discussion hall. Ideas I've got some far: some sort of constellation puzzle, a bunch of special keys that must be collected. Information based puzzle based on the dragon God pantheon, a bunch of mirrors that reflect secret switches. Only one dungeon will actually have the well, gonna have them fight through at least 2, then a ha-naga as a final boss at the well. Any ideas for my puzzles or creative ideas for gaining entry to these central chambers with the ideas I already have?