Windows Embedded Compact Application Development
Microsoft moved most of the Windows CE documentation to https://docs.microsoft.com/en-us/previous-versions/windows/embedded/gg154201(v=winembedded.80), and it is not indexed by Google.
Application development for Windows CE is a straight forward affair. The development tools are the same tools you would use to develop a application for a PC running a desktop version of Windows. However, instead of running and debugging the code directly on the development PC, the application is deployed directly to the Toradex module (aka the "target"). The connection to the target is typically via USB or Ethernet.
It is even possible to develop applications which run both on an x86 development PC and the Toradex module if your application is written in managed code to run under the .NET Compact Framework.
Windows Embedded Compact 2013
WEC2013 requires Visual Studio 2012 or Visual Studio 2013. The Community Edition of Visual Studio will work too. The Community Edition is free in many cases (see terms for details).
Application debugging is done via an Ethernet connection.
WEC2013 is not available for the Colibri PXA line or for the Colibri T20 (Nvidia Tegra 2).
Windows Embedded Compact 7 and Windows CE 6
WEC7 and WinCE 6 require Visual Studio 2008 or Visual Studio 2005. Application debugging is done via USB client (Windows Mobile Device Center) or Ethernet. You will require at least the Professional Version or higher.
Make sure you install all the patches listed in this Article
Learn more in How to Setup the development Environment for VS2008.
It can be tricky to find & purchase an older version of Visual Studio; see our guide for recommendations: How To Purchase Visual Studio.
Toradex provides free samples and libraries to get you started.
Graphical User Interface
Very popular are Windows Forms, Silverligth/XAML in .Net CF or the Qt Framework. You find more information in the Graphical User Interface Article.