It's been a while since I put up some megadungeon "best practices." I've discovered a few more in the process of designing, running, and maintaining my megadungeon, Felltower.
Avoid Useless Choices
Providing alternative ways to get around a dungeon is great.
Providing distractions and false paths adds to the dungeon experience.
But, in general, avoid too many useless choices. That is, a choice between A and B when A and B end up the same way. Two hallways leading to the same area is generally okay, but two doors to the same room, from the same other room? Useless. It just kills the most valuable resource - real world playing time. Provide alternatives without providing an excess of choices that don't actually make a real difference.
Avoiding this is as simple as asking yourself - is this an alternative, or a choice that won't matter in actual play?
Understand the Space Between Your Places
Players are resourceful, and some game systems - GURPS is one of them - provide them with a lot of resources for making their own passages in a dungeon - Shape Earth - or determining where to go - Pathfinder, Seek Earth. The depth between levels, the relative angle of passages, the nearest source of X from area Y - you'll need to know these. It's worthwhile to note this on your GM master maps so you don't get stuck when the PCs need to know how far down stairs go, the depth of a shaft, the thickness of a floor, etc.