Yesterday (Jan 15th, 2014) Oracle support came up with a patch for JDeveloper in concern of running ADF applications using IE11.
Form Article Id 1599898.1:
Below is a list with available patches for IE11 issues. The list will be updated once more patches become available. However this does NOT mean IE11 is certified but the patches allows you to access the application IE11:
patch 17236592 – IE11 SUPPORT: ADF APPS DON’T LOAD WITH IE11
Patch to avoid the popup shown above from appearing.
Versions: 18.104.22.168.0, 22.214.171.124.0
You need a support contract to get the patch.