... only in specific virtual desktops? e.g. if i run vncviewer in one virtual
desktop, i may want it to cover the panel so i can see the entire virtual
screen without scrolling. but if i switch virtual desktops, i don't want the
panel to be covered by an emacs or konsole window.

/mark

I don't think this is possible at the moment. Have you tried to make the vncviewer window fullscreen instead? (Right click on window title -> Advanced -> Fullscreen.) You can also make it to always start in fullscreen mode (Right click on window title -> Advanced -> Special Window Settings... -> Geometry -> check Fullscreen -> Apply initially -> check.)