Nice work about the Stats - that was one of the issues on my list.
At some point the specialised searching templates (see User:Claus chr/Search and User:Claus chr/DPL) stopped working - they have been tweeked to work again, but the DPL extension that we use is very old and has been superseeded by DynamicPageLoad 3 (which requires a newer version of the wiki software).
The WhatLinksHere tool in the right margin does not work reliably.
Perhaps my biggest issue is with the translate extension. Sometimes pages that needs updating fails to show in the Special:LanguageStats page. There are other glitches in the translate system, but hopefully they will all be resolved when that extension is updated.