1. On ffxi.allakhazam.com/wiki/ : Space between categories far too large. To correct, possible use just headers for main page only with arrows much like the side bar to browse content. Example
2. Inconsistancy between main pages and subcategories. For your main page, you are using <ul> and <li> tags under each heading. But when you go to the subcategories, such as Areas, the subcategories for it instead have <br> <br> between each one. While this doesn't necessarily effect the function, it is something relatively simple (though time consuming, I'm aware) to fix.
3. As well as this, the inconsistancy between each subcategory in terms. I mentioned this to NixNot, but he wasn't really sure how to fix it. But some subcategories have the “Category†listed at the bottom of the wiki text, and other pages do not. I'm not sure if there is an easy way to do this, but it wouldn't hurt looking into. (I know this can sometimes drive me batty with other sites as I'm trying to research a lot of info in a short time.)
4. The “Content†boxes throughout the wiki have an odd placement.Content menu could be placed at the top of the page above the right ad banner. What it looks like now. What it could look like.
5. I am unsure if this is just the way wiki works and there's no way to change it. But I also was disappointed when clicking the Category link for “Final Fantasy XI†that it took me to all categories and articles instead of back to /wiki/. Though, thinking about it, this may be because you're running several different wiki categories off the same database? Is this correct? If so, you can ignore this point. It just means while it's in beta, it'll be difficult to get back to the main FFXI wiki page.
This is all I saw that I knew how to put it into words. Other than that, the feel of it (I'm not sure if it's the colors or what) just seems off. Maybe it'll strike a better chord once it's out of beta. If you don't like my suggestions, that's fine too, but I was told I should go ahead and post what I thought.