I've had a good experience with using [Scalar](http://scalar.usc.edu) as a reference work - you can describe a place and link all the organizations, people, and smaller places within it, but then you can also look at your "people" tag(s) when looking for an interesting NPC, your "low-level" tags when looking for a challenge for a new party in the same world, etc. More useful the larger your world grows. The features that distinguish it from similar tools IMO:

1) When you hover over an internal link, a short description pulls up, so you can say "the tower has three *guards*" and when you hover over guards, you see their brief combat stats, provided you've set that as the description on the *Guard* page. 
2) You can upload images and annotate specific areas of the pictures with whatever you want, including links. So you can have a dungeon map with little hover-reminders for you of what encounters take place in each room. 
3) You can embed media, like YouTube videos, either at a specific spot on the page or so they follow you down the side. Useful for soundtrack switching.

It's not the best for quick editing in place, though, so I use a [GDoc](http://docs.google.com) to keep track of changes, then go back and edit them in during a break or after a session.