Well, since this is turning to a hints'n'tips thread...
When I want to take a shot of a specific window, I'm way too lazy to crop it myself. I have Xorg, netpbm installed, so I just do
xwd | xwdtopnm | pnmtopng > pic
and click on the window I want in the pic. Nothing else, no cropping necessary. No window borders either unless an option is given to xwd.