GIMP
GIMP (GNU Image Manipulation Program) is a free and open source image editor. Download it from gimp.org.
Usage with Source
VTF
There is currently no VTF plug-in for GIMP. Save as TGA instead, then import.
RGB of transparent pixels
GIMP's developers consider the alpha channel to be transparency. Source (and DirectX/OpenGL in general) generally don't.
This means that GIMP is quite happy to destroy or not operate on RGB color information for pixels with 0% alpha, causing horrendous problems in most 3D engines. Aside from the obvious lack of color information, the behaviour leads to the "halos" sometimes seen around the edges of filtered materials.
Luckily, so long as Layer masks are used, in current versions of GIMP the only operation known to trigger the problem is the Merge Layers command. Unfortunately it's used almost every time one exports some work!