xwininfo
The X11 tool for pointing at a window and finding out what it actually is: id, size, position, depth and visual.
Run xwininfo and the pointer turns into a crosshair; click a window and you get its id, absolute and relative position, width, height, border width, depth, visual and map state. -tree dumps the whole subtree, -root targets the root window, and -id spares you the clicking.
It belongs to the same family as xprop, which shows the properties, xev, which shows the events, and xkill, which ends the owner. Its output often reveals that what looks like a window is a frame the window manager wrapped around the real one — lesson one in why debugging X takes longer than expected.