I'm using ikiwiki to build this website, both the regular parts and the blog and I'm quite happy with it. Before, I used to use wml for that, and at that time I even developed a lot of personal extensions ton WML (I was grad student
Things are quite simpler with ikiwiki, and I don't had to hack that much to get it working. That's almost matching my taste now, even if the page footer is still ... improvable. This page lists the most notable things I've done with ikiwiki so far. If you have comments, they are always welcomed, and I'll even try to help you if I can. Actually, only the first hack really relates to ikiwiki, but the other could
Nice hierarchical navigation bar
I was quite unhappy with the navbars provided by default by ikiwiki, and none of the proposed plugin really convinced my either. I thus hacked one of them to make it fit my own taste. I simple hold this navbar.pm in my plugin directory. It parses the menu structure from a separate file, named navbar.mdwn (historical name, sorry) Rename this file from navbar.configuration to navbar.mdwn (I'm changing its name to avoid issues on this very page), and copy it to your the root directory of your ikiwiki installation.
I think that this is it. I can't remember whether I modified the page template because that's quite some times that I did it and I didn't "document" it on time. I'd be glad helping you if the script fails on you.
Enforcing ASCII encoding
Something is broken around the encoding of my pages. I'm not quite sure where the problem is, because it works fine on the local webserver I use to preview my pages, but not on my lab's site. Since I didn't manage to fix the issue, I decided to get violent and configured git to convert any non-ascii char of my site into html encoded entities. All details are here (in French, but you should get it from the scripts).
Sharing pdf slides without proprietary web 2.0 software
Another plugin missing in ikiwiki is pdfshare, something allowing to share pdf presentations on your pages directly, without having to use crude proprietart stuff such as slideshare or similar. I hacked something here using the hints of the ikiwiki bug report above, but I didn't manage to integrate it properly to ikiwiki unfortunately. Check this blog entry for more info.