 <p>To start an app you need to call <a href="http://msdn.microsoft.com/en-us/library/aa922104.aspx" rel="nofollow"><code>CeCreateProcess</code></a>. Registry access starts with <a href="http://msdn.microsoft.com/en-us/library/aa922104.aspx" rel="nofollow"><code>CeRegOpenKeyEx</code></a> (there are reads, writes, etc too). All of these are also wrapped in managed code in <a href="http://rapi.codeplex.com/" rel="nofollow">this open-source library</a>.</p>