>When upgrading from Windows Server 2008 to 2012, is the recommended way to simply upgrade or install from fresh?

In-place upgrading is better than it used to be e.g. http://blogs.technet.com/b/chrisavis/archive/2013/10/01/performing-an-in-place-upgrade-of-server-2008-r2-to-server-2012-r2.aspx

One might argue it depends on the complexity of the current server. But that's a two-edged sword:

- The more complex the current setup, the greater the chance something will go wrong in the upgrade, and it might be a PITA to troubleshoot

- But, the more complex the current setup, the greater the chance you'll miss something setting up a new, clean install. And it might take a long time to get everything set up like the old system

An in-place upgrade may not be possible if there are any incompatibilities. For example, SQL Server 2005 is not compatible with Server 2012 or 2012 R2: https://support.microsoft.com/en-us/kb/2681562

In a perfect world you would have complete instructions on how to set up your desired environment on a new server, so it would not be too onerous to do a fresh installation. But, an hour for an in-place upgrade is hard to argue with.

If you could spare an hour you could test the in-place upgrade first. If that doesn't work, blow it away and do an install from fresh.