Vistaprint (www.vistaprint.com) has a hugely successful MediaWiki system internally. 150,000+ topics, 1000+ active users across several continents, five years of history, and a fully supported team of developers to create extensions. (We are looking into open-sourcing some of them.)
The main requests from our corporate users are:
0. WYSIWIG editor. No surprise here.
1. A desire for a department to have "their own space" on the wiki. I'm not talking about access control, but (1) customized look & feel, and (2) ability to narrow searches to find articles only within that space. The closest related concept in MediaWiki is the namespace, which can have its own CSS styling, and you can search within a namespace using Lucene with the syntax "NamespaceName:SearchString". However, this is not a pleasant solution, because it's cumbersome to precede every article title with "NamespaceName: " when you create, link, and search.
If the *concept* of namespaces could be decoupled from its title syntax, this would be a big win for us. So a namespace would be a first-class property of an article (like it is in the database), and not a prefix of the article title (at the UI level). I've been thinking about writing an extension that provides this kind of UI when creating articles, searching for them, linking, etc.
Some way to search within categories reliably would also be a huge win. Lucene provides "incategory:" but it misses all articles with transcluded category tags.
2. Hierarchy. Departments want not only "their own space," they want "subspaces" beneath it. For example, "Human Resources" wiki area with sub-areas of Payroll, Benefits, and Recruiting. I realize Confluence supports this... but we decided against Confluence because you have to choose an article's area when you create it (at least when we evaluated Confluence years ago). This is a mental barrier to creating an article, if you don't know where you want to put it yet. MediaWiki is so much better in this regard -- if you want an article, just make it, and don't worry where it "goes" since the main namespace is flat.
I've been thinking about writing an extension that superimposes a hierarchy on existing namespaces, and what the implications would be for the rest of the MediaWiki UI. It's an interesting problem. Anyone tried it?
3. Tools for organizing large groups of articles. Categories and namespaces are great, and the DPL extension helps a lot. But when (say) the Legal department creates 700 articles that all begin with the words "Legal department" (e.g., "Legal department policies", "Legal department meeting 2012-07-01", "Legal department lunch", etc.), suddenly the AJAX auto-suggest search box becomes a real pain for finding Legal department articles. This is SO COMMON in a corporate environment with many departments, as people try to game the search box by titling all their articles with "Legal department"... until suddenly it doesn't scale and they're stuck. I'd like to see tools for easily retitling and recategorizing large numbers of articles at once.
4. Integration with popular corporate tools like MS Office, MS Exchange, etc. We've spent thousands of hours doing this: for example, an extension that embeds an Excel spreadsheet in a wiki page (read-only, using a $10,000 commercial Excel-to-HTML translator as a back-end), and we're looking at embedding Exchange calendars in wiki pages next.
5. Corporate reorganizations and article titles. In any company, the names and relationships of departments change. What do you do when 10,000 wiki links refer to the old department name? Sure, you can move the article "Finance department" to "Global Finance department" and let redirects handle the rest: now your links work. But they still have the old department name, and global search-and-replace is truly scary when wikitext might get altered by accident. Also, there's the category called "Finance department". You can't rename categories easily. I know you can do it with Pywikipedia, but it's slow and risky (e.g., Pywikipedia used to have a bug that killed <noinclude> tags around categories it changed). Categories should be fully first-class so renames are as simple as article title changes.
Hope this was insightful/educational... DanB