Tools I'm Using

C# through the VS.net IDE
DirectX 9.0 api
Notepad for design documents and the like written in xhtml
Doxygen for all my commenting needs
A blog from blogger to record my progress

Graphics and music are just stand bys until I get to a stage where I need to start making these look a little more professional.

References Used

Books

Software Engineering For Computer Games - see book recommendations for more detail info.
Special Effects Game Programming with Direct X, despite the name this is a resonable introduction to Direct3D and I've found it quite useful.

Websites

MSDN Library DirectX - offical DirectX docs
BuffPortion - Handy information about creating a full screen DirectX app using C#
Enginuity - GameDev tutorial about creating a 3D engine from scratch, using C++
Extreme .Net Forums - slow forum about game design using the .Net framework

2D Engine using 3D API info

2D Rendering in DirectX 8 - GameDev article uses C# and an early version of DirectX but still very handy.
... I had a number of these links but it seems I've failed to save them all.