I was trying to open one of my old projects build with VS2008 and it has a class library targeted for Windows Mobile 6 devices (.NET Compact Framework 3.5). Since the good old V
Not certain where this "everywhere" is that you're reading, but it's wrong. Compact Framework 3.9 has not been released yet. It will be released when Windows Embedded Compact (Window CE) 2013 is released, which should be in the first half of this year (2013).
Even when it is released, you still will not be able to use Visual Studio 2012, or Compact Framework 3.9 for an earlier version of Windows CE. The tools and compiler will be for 2013 only (not saying I agree with or like this, just reporting the facts).
If you are targeting WinMo 6.x, your only option today is CF 2.0 or CF 3.5 with Studio 2008, and I don't suspect that will change, even when a new version of the CF is released.