Cmd-Shift-4 allows you to select a portion of the screen to screenshot. If you press Space after, you can select whole windows.

The thing is upshot doesn't seem to trigger if portion of the screenshot is selected. Capturing the whole window works though.

Edit: someone has opened a github issue for this https://github.com/fwenzel/upshot/issues/28

Yes this was unintentional. Thanks for reporting this, I'll look into it!

I'll also need to add automated updates soon, or I can't notify people of updates ;)