I can't speak to the websites having problems with IE9 and above, however the desktop application compatibility situation has ended up being overblown in my exp

I can't speak to the websites having problems with IE9 and above, however the desktop application compatibility situation has ended up being overblown in my experience. Sitting down with "Process Monitor" and weakening permissions or spending a few minutes figuring out how to apply the existing Application Compatibility shims the OS provides has sorted out almost every problematic desktop application. For the few applications that failed to yield the "Windows XP Mode" VM (which comes with Windows 7 Professional licenses) has worked fine (albeit the multiple users per PC "story" for "Windows XP Mode" is terrible and having a bunch of XP VMs to support adds complexity).