Pointsy is a simple GUI app for marking points on an image (or two images, displayed side by side).
Pointsy can be used for marking rectangles and paths too, since points are displayed with horizontal and vertical rulers, or with lines connecting them.
You can then feed these points to some other tools.
(A very similar app is panopoints, which unfortunately uses the deprecated Gtk 1.2.)
Pointsy is provided with a few example scripts (which all use
ImageMagick's convert):
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crop: Crops an image. (There's also the crop-from-points script.)
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join-on-point: Stitches two images based on a point they have in common (e.g., useful for joining two halves of a big newspaper page scanned with a common A4 scanner).
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levels: Like the similar tool in GIMP. You're shown a histogram and you need to mark two points in it (for "black" and "white").
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balance: If your scanner produces reddish or bluish images, this tool lets you fix them by marking a rectangle that's supposed to be white (or grey).
When dealing with many images, these scripts are easier to work with than a full-blown image editor (as GIMP or Photoshop) because you doesn't need to mess with menus and dialog boxes. You just need to select a couple of points, press Enter, and you're done.
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Lua modules: lgi, Penlight, LuaFileSystem (because of Penlight). Tip: if you're on a Debian-based system, do
apt-get install lua-lgi lua-penlight lua-filesystem -
Lua 5.1 or 5.2 (there's going to an issue with Lua 5.3 as the point coordinates are float values and the example scripts use "%d").
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Gtk 3