fun times. just wrote the wiki today. With the separate rgba node; each output channel is a BW image showing the intensity of that electron gun. The alpha is a BW image as well. So you could feed a channel in as an alpha, and thus have all the blue things in a picture become invisible, with green things partially visible (since they are blue and yellow). You could even have like two completely different images alpha each other out.
To do what I think you want and use a mask, create a black pic with a white circle. Like you said, black is zero is alpha zero is transparent. I created a white sphere in front of a black shadeless plane; that way I can move the sphere around. Feed that into the TOP socket of a color mix node with the Multiply function. Set the Factor to 1. Feed your picture into the Bottom socket. So, Top image pixel black=0 times bottom color Red times factor 1 = 0 and it comes out black. Where a top mask pixel is white=1, times the bottom pixel (say Green) times factor 1 puts out Green. Blurring the circle edge of course creates a softness at the edge.
With factor=1, top and bottom location is irrelevant. However, the default factor of .5 tries to mix the image with the mask if they are reversed. curious.