well, i can only look at from a viewpoint based on my ( very limited! ) experience with programming for older windows platforms, i.e. 9x & ME.
the transparency i am doing is done on certain portions of the windows that are fully under my control, that is, the ones that i am creating from my own program. even then, it is nowhere near true transparency. rather, it is simply grabbing a picture of the screen underneath, blending it with my window, and then displaying it as my window background. granted, it's fancy enough to update smoothly when the window is dragged around the screen, making it look truely transparent. sort of a cheap trick.
what you are after is far beyond what i can do as of yet, and i'm pretty sure couldn'tt be done on anything below windows 2K.
above that though, it may be possible. one idea is that perhaps you could make the non-client area transparent. or certain parts of the client area. ( identifing by handle maybe? ) the thing is, is that i'm not really sure how the transparency support works on 2K and up. so anything could be possible, but i really wouldn't know.
i do know that whatever you used would have to hook into the program you desire to be changed, and therefore is pretty much outside of the scope of Visual Basic.
sorry i couldn't be more help on this.