Firstly I recommend reading this:
http://hackslashmaster.blogspot.com/201 ... -trap.html and just about everything else on the blog. As opinionated and self-righteous as it might be; there is usually some truth behind it and it is always well thought out.
Now onto what works for me.
I tend toward two methods for making dungeons that don't follow the 5 room method. They each have their pros and cons, and I often mix them.
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The "Makes Sense" Method. This sort of mimics what has been said.
1. What was it originally?
2. How and/or why did is it different now?
3. What is there now?
I hardly ever go into much detail about the first two. They aren't usually that useful, unless it is a relatively "new" dungeon (e.g. a monastery recently overrun by undead). However it helps me think of challenges and Easter eggs to put in that show (rather than tell) what might have happened.
An example is the Mines of Moria.
1. It was a Dwarven stronghold and mine.
2. They dug too deep and unleashed something terrible.
3. Hordes of orcs and other unmentionables live there now; mostly unknown to the fellowship.
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The Metroidvania Method.
After analyzing the titular video games I realized why I found them fun (This would probably warrant an entire discussion on it's own).
Here I just think of things I want to put in. These usually follow the traditional "monster, trap, treasure, trick, and special," but can be anything of interest. These become my "centerpieces." I then take some paper and mark where they are. If it's an entry way it's probably near the edge, whereas a vault might be near the center. Then I connect them in a semi-logical way with lesser rooms and intersections and twisting paths in between and I'm basically done. It's important to have the lesser rooms because they add suspense for the party, and give me somewhere to put anything I might think of later.
*Note: no room should be empty unless the room is the centerpiece itself. Even then it should be set apart from the other places in the dungeon.
Also centerpieces don't have to be big; they just have to be interesting. A skeleton by a small pool of water in some "side room" will be interesting to most players. Is the skeleton animated? Is the water poisonous? Is there something in the water the party might want?
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Now when I make a dungeon I typically use a bit of both methods. I think of things I want in the dungeon, then I think about what the dungeon is, which gives me more ideas. Even if I'm not using the
makes sense method explicitly, my dungeons often have a theme that helps tie everything together, and the same sort of thinking helps to flesh out and rationalize my ideas.
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A final note: What story (if any) do you want to tell? If the story is completely based around the player's actions then you probably don't need much in the way of backstory. But if you want to show a piece of the world, then you will need
something for the players to discover and piece together. After all it is a game, and some players see the story itself as a reward. For more on this the YouTube channel Extra Credits recently made a video about story telling and information density which you can find here:
https://www.youtube.com/watch?v=ghrI2Vb ... J6OCk1XB1p.