Obviously, I make extensive use of my wiki. One aspect of the wiki way I particularly dislike is the requirement for explicit linking. If I am writing about George Bush, I have to either write his name as a WikiWord (e.g. GeorgeBush) or put square brackets around it (e.g. [GeorgeBush]).
What this means is that pages end up relatively weakly interconnected. I might casually mention my research on one page, but it won't be associated with my Research page unless I link explicitly to the exact title. And honestly, who wants to keep track of all the pages in a wiki and their precise names? Wouldn't it be better if...
And so on. One way to do this would be to take an indexing/implicit search system like Dashboard and have it run through things as we add them to our information stores, identifying related content and linking things up where possible. Dashboard works slightly differently--it displays actual information as well as links in a sidebar--but association process would be the same.
Of course you would only want to link things up when you had relatively strong results. So the phrase 'modality todo-list' would probably match up 100% with my Modality todo wiki page, and nothing else, indicating that a direct link to that page would be appropriate. Niamh's name, on the other hand would likely match all over the place, but link very strongly. Thus a link to a search results page would be more appropriate. On the other hand, a casual mention of, say, Alan Greenspan in a blog entry wouldn't necessarily merit linking every other mention of him to that entry. The algorithm would likely require some revision.
I also think that Wiki pages should allow comments at the bottom. Otherwise active pages get cluttered up with back and forth that no one really has the authority to clean up. Comments would be kept separate and could just sit there forever, and if people reach a conclusion in the comments that necessitates revising the page they can go ahead and do that.
It might also be nice to have a per-page password protection. So I could mark a page with a password and then just give it to whoever I wanted to be able to view it. The other alternative would be to have full usernames and groups and per-user permissions, but that seems harder.