Shamus Young makes some good points on dungeons that make sense.
I know I am being bit of a salesman here but two years ago I got the project of redoing the old Judges Guild module Fortress Badabaskor for D&D 3.5.
The original definitely had it charm and strong points but it had a healthy dose of a orc in the ten by ten room syndrome.
I pride myself on being able to keep 90% of the original, revising it with 3.5 stats and making the dungeon make sense as Shamus points out.
However to some doing this kind of work may seem disrespectful. Shamus' point of view is that by adding realistic detail that it opens up more ways for the players to resolve the adventure. Offers a greater scope for their imagination to play in.
But it is more than that. It doesn't just help the player side but the DM side as well. One of the fundamental things we do is adventure. The only way the players are going to adventure is through what you, the DM, provide for. By incorporating realistic elements both in setting, NPCs, and plot you increase the points of conflict. More conflicts means more opportunities for adventure.
Also the old saying that realism has it's own truth is particulary pertinent. By using Realistic elements players can use their common sense knowledge to make valid assumption about the situation or npcs.
Of course to much then you get the infamous cow incident that sunk Harnmaster forever in the eyes of my friends. That a story for another time. For now I will say too much of anything can harm.
For Badabaskor it was a continual balencing act between keeping the old elements and making them make sense.
You can find both version of Badabaskor online; the original and my version.
And a preview of the fourth level here
The ultra-cool dwarf and the seven planets
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