I've ported Sam Phung's CE registry editor, as on Codeplex to Compact 2013. Source code is there as well as binaries.
The source contains VS2008 and VS2012 project files so it can be seamlessly used to build for Windows Embedded Compact 7 or. Compact 2013 (Compact Framework 3.5 or 3.9).
As its Managed Code (C#) with no PInvokes it works on ARM and x86.
It will be included in next release of Compact13Tools (V3,0) coming soon.