In my quest to un-metro Visual Studio I've found that the basic toolbox icons for HTML (MVC & Web Forms) and Win Forms are stored as bitmap resources in a number of unmanaged DLLs. WPF and others are stored mostly as PNG and ICO files in the newer managed DLLs. The managed resources are a combo of directly embedded files as well as serialized Bitmaps, PNGs, Icons, Image List Streams, and binary Streams.
Take a look in these files for most of the toolbox images
\Microsoft Visual Studio 11.0\Common7\IDE\1033\Microsoft.VisualStudio.Windows.FormsUI.dll
\Microsoft Visual Studio 11.0\Common7\Packages\htmled.dll
As for how the color is modified, it looks like Visual Studio replaces white with black, along with changing shades of white/grey to their darker counterpart while leaving the rest of the color alone. In years past they've included a style guidline document along with the SDK. I haven't found one yet for 2012 and their MSDN link still points to the 2010 document.