For all posts related to megadungeons, both theoretical and relating to my actual game play, try the megadungeon label on my posts.
What is a Megadungeon? - a post on defining a megadungeon. What do you need a definition for? It helps you focus on what's important to include, and what will trip you up if it's missing.
For my posts about megadungeon design and operation:
Mapping My Megadungeon (Comments have links to good resources)
Megadungeon "best" Practices
Part X: Room Descriptions
Part XI: Multi-Room Encounters
Part XII: Paper Size
Part XIII: From Around the Blogs
Part XV: Themes, Knowledge, and Links
Part XVI: the Usually Principle
XVII - Lethal Entrances
Megadungeon Lessons From The Pyramids
Also, here is one about megadungeon exploration:
Megadungeon Exploring: Three Do's and Don't's"
And another about player impact on the megadungeon city:
Player Impact on the Megadungeon City
Dungeon Trick Features
Dungeon Trick Features: Sloping Passages
Dungeon Trick Features: Spinners
June Megadungeon musings
Reflections on Megadungeon Play - Immediate and Cumulative
Resource and Planning Tips for Delving
Random Thoughts X has some links to "fast" and "slow" dungeon level articles.
Some Myths of Megadungeon Play
The Problem with Other People's Megadungeons
More thoughts on Megadungeons
Other People's Articles
Jaquaying the Dungeon (at The Alexandrian)
Megadungeon Links (at The Rusty Battleaxe)