I've tried adding registry entries at:
Hive: HKEY_CURRENT_USER
Key Path: Software\Policies\Microsoft\Internet Explorer\BrowserEmulation\PolicyList\
Value name: sub.companyname.com
Value data: sub.companyname.com
However in Internet Explorer 11 this method does not work as it seems the list has moved.
My.Computer.Registry.SetValue("Software\Policies\Microsoft\Internet Explorer\BrowserEmulation\PolicyList", "sub.companyname.com", "sub.companyname.com")
It appears that under Windows 8.1 Enterprise/IE11 the entry is a binary one - this is where I see the entries added under Tools/compatibility View Settings in the registry on my system:
HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\BrowserEmulation\ClearableListData
Look for a Binary value called UserFilter - it's a bit hard to read when you look into it but you can tell it holds your entries.
We have several sites we'll need to add to the list so most likely will export the list from a "master" computer then push it through Group Policy Preferences at least once for initial settings. Unsure how we'll script additional entries at this point so that when users add their "personal" settings we don't overwrite the value but append to it but one thing at a time I guess.