MODERATORS NOTE: This effect may have issues with newer versions of Paint.NET.
An alternative plugin, called Apply Alpha Mask, is available here:
https://forums.getpaint.net/BoltBaitPluginPack
Alpha Mask -- 2.0
AlphaMask.zip
Version 2.0 adds the ability to use whatever image is on your clipboard.
The supported image types at the moment is kinda sketchy, but the kicker is it works for stuff copied inside Paint.NET, which is 99% of this plugin's use, anyway.
This plugin allows you to import an image from a file or the clipboard and make it an alpha mask. If the image has color, it will be converted to greyscale.
Clipboard idea courtesy BoltBait.
Source Download, 2 years later
AlphaMaskImport - Source Code
Old description / links: