Windows 8.1. Update 1 introduces a new feature called Enterprise Mode for IE11 (EMIE) that allows Microsoft's latest browser to work better with older coded web sites.
I wrote recently about how it works and how Enterprises can use it in Managing Web Site Compatibility in Enterprise Mode for IE11. Read through that article to get a good feel for the capabilities and also how to centrally manage web site and web app compatibility.
Part of the central management solution is a special tool called Enterprise Mode Site List Manager that is required to properly create and manage site compatibility lists. At the time I wrote that article the tool was yet to be publicly released. The tool is now available for download from the Microsoft Download Center.
You can get it here: Enterprise Mode Site List Manager
And, to further manage IE11 in your environment, you'll want to also grab the just released Group Policy templates: