My personal favorite is TWiki. It has some nice features like file attachments, a great search interface, high configurability, and a rich set of available plugins (including an XP tracker plugin.)
One cool thing about TWiki: configuration settings are accomplished through text on particular topics. For example, each "web" (set of interrelated topics) has a topic called "WebPreferences". The text on the WebPreferences topics actually controls the variables. Likewise, if you want to set personal preferences, you set them as variables–in text–on your personal topic. It’s a lot harder to describe than it is to use.
There are some other nice features like role-based access control (each topic can have a variable that says which users or groups can modify the topic), multiple "webs", and so on.
The search interface is available as variable interpolation on a topic, so something like the "recent changes" topic just ends up being a date-ordered search of changes, limited to ten topics. This means that you can build dynamic views based on content, metadata, attachments, or form values. I once put a search variable on my home topic that would show me any task I was assigned to work on or review.
I’ve also been looking at Oahu Wiki. It’s an open source Java wiki. It’s fairly short on features at this point, but it has by far the cleanest design I’ve seen yet. I look forward to seeing more from this project.