Well, in GIMP (the drawing program I use that is FREE. <3), when you create a new image, there's an Advanced Options area and then you can change the Fill In to transparency. Haha. I don't know for other programs, but for sure there's transparency there. Haha.
I use GIMP too. (hail GIMP) I use the 'color to alpha' to get transparency. The problem I have is when I upload the picture to dA, the transparent areas are black instead. I've tried GIF, JPG, and PNG type images but none of them seem to retain the transparency.
Well, usually it's PNG. It should retain the transparency; however, you have to have all of your layers need to be merged/together, which sucks and causes you to save a XCF file if you need to access those layers after saving (my GIMP crashes every time I open it the first time. so I save constantly.)
Well I always save an XFC as a back up for multi-layer pieces, just in case.
I uploaded this([link]) piece as a PNG and you can see how well it didn't turn out. Only the tendrils in the middle were supposed to be visible and the rest transparent. It also caused that disgusting noise around the core.