http://blog.jquery.com/2015/07/13/jquery-3-0-and-jquery-compat-3-0-alpha-versions-released/
Please check your code for how you use the .show() and .hide() methods!
I did a quick grep for a 2.6.9 site (has a dozen random modules) and the .js files listed below were using .show(). It might well be that some of them will break with jQuery 3.0.
BatchChildEditor.js
ProcessBatcher.js
AdminThemeReno\scripts\main.js
InputfieldFile.js
InputfieldPageAutocomplete.js
InputfieldSelector.js
JqueryTableSorter\widgets.js
JqueryWireTabs.js
ProcessField.js
ProcessModule.js
ProcessPageAdd.js
ProcessPageEditImageSelect.js
ProcessPageEditLink.js
ProcessPageList.js
ProcessPageLister.js
ProcessPageSearch.js
ProcessTemplate.js
SystemNotifications\Notifications.js
templates-admin\scripts\inputfields.js
templates-admin\scripts\main.js