Are there any PDF viewers (Windows, OS X, or Ubuntu) that enable you to see the page-relative pixel coordinates (x,y) of your cursor? I know Photoshop can do this, but I'm looking for something light-weight and cheap (or free).
I don't know about PDF readers specifically.
However a couple of general solutions:
Windows: autohotkey has tools for pulling window relative coordinates so one just needs to negate toolbars etc.
Linux: On X11 systems a tool called Xev is available that displays all X11 events including cursor movement and it can be told to be limited to a particular window ID gained via xwininfo.