Windows Mobile 6 devices come with .NET Compact Framework 2.0 in ROM and also expose .NET APIs for a lot of things (camera, system notifications, email, contacts, ...).
I'd recommend using Visual Studio 2008 and the refresh version of the Windows Mobile 6 SDK, which includes emulators, documentation, tools and samples.
Besides MSDN, a good resource for Windows Mobile samples is Chris Craft's Blog, who recently built 30 mobile applications in 30 days. There are samples for a lot of different techniques which you can use for a jumpstart.