If you have been using Visual Studio 2005 with Windows Mobile 6.0 SDK, you will notice that after you install VS 2008 Beta 2, you don't see the templates for this SDK in the New Project Dialog for Smart Devices.
You attempt to repair the SDKs, but still no luck.
So here is what is happening.
A device SDK needs to register with a specific version of the development tool when you install the SDK. This is done by making a Call to what we call the SDK Installer Shim. During Install and Un-Install a call is made to this shim to register or un-register the SDK. Also when repair on the SDK is called, it should make a call to the Shim. *however* the WM 6.0 repair logic did not make the call to the shim. So no matter how many times you repair the SDK, the templates won't show up.
To fix it, just un-install and re-install the SDKs. If you had VS 2005 and VS 2008 Side by side, everything will still work as expected and you can either of the development tool to build applications for this SDK.
The advantage of using VS 2008 would be that now you can use NETCF 3.5 to target the WM 6.0 Devices, as well as take advantages of new Unit Testing features for device developers which are available in VS 2008.
I do want to clarify that VS 2008 only ships with Windows Mobile 5.0 SDKs in the box. You would need to download Windows Mobile 6.0 SDKs from here.