I'm building an application that's a host of various other applications (of sorts). One of the features I wanted to try and achieve was the possibility of running Windows Mobile applications. I know an emulator can be downloaded from MSDN but everything suggests it is only really for testing Mobile apps.
Would it be a possibility to start and control the emulator in a child window of my own application using .net?
The WinMo emulator is really Device Emulator (though a newer version), which is rooted in Virtual PC. You might look at the Device Emulator source (even older, but it might give some hints as to how it's hosted), but my guess is that you're going to have to hack it, finding the emulator's host window and reparenting it. You can change it's skin, which might also be useful.
What kind of application do you want to run?
.NET Compact Framework apps will run on the .NET Desktop Framework.
Here's an example of an app compiled against the .NET CF. First image is it running on the emulator, second is running on the desktop framework directly.
You can control the Device Emulator program via a COM interface. See here for more information.