Main Page slider functions (it'll now open each slide's template page when clicked upon)
"Edit summary" auto-filler box
Auto-refresh on Wiki Activity, new files lists, logs, watchlists, contribution lists, etc.
The show/hide button on some infoboxes and tables
Wiki staff tags
The "Back to Top" button in the bottom toolbar
A few others that shouldn't affect wiki activity here too much
EDIT: I also recently noticed that "verbatim" tags have also been disabled, which is the tag that converts extra code for widgets and modules, like our Twitter feed. These will also be disabled until further notice.
Update: JS and Verbatim will work again later tonight. However, it will only be in read-only mode, meaning it can't be edited. Pages in the MediaWiki: namespace will also be in read-only mode, with the exception of local CSS. This change will be indefinite for the time being, with the earliest predicted time frame being later this week.