SS of jdesk will look just like the one with Clickonic (minus the icons ofc), except the black area is the size of whatever you set WorkArea to. With the workarea set to what it normally is (0 21 0 -21) the black area covers the whole visible screen, so Milkdrop doesn't show up at all. (I have my desktop set to straight black atm for testing, normally the wallpaper shows up on jdesk and would be covering Milkdrop too)

BSPlayer in desktop mode works for me too.

After some reading and digging through the xLabel source I found out why mouse clicks aren't registering on a transparent label. It's a problem with the Windows API itself, when a window has its transparency set to 0 it automatically ignores mouse clicks. Sigh.