Use TGA, load time is faster. Easiest way to deal with shaders is that unless you're doing something totally new try finding something that has a similar effect to what you want and edit that shader to use your images.
I hate TGA. I'll use PNG over TGA any time if I can help it. Too complicated when you can just delete sections rather than deal with the alpha channel stuff.
And yeah, I ended up using DT's shader from his ESB Luke.