Free and open source

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets. 

Perform morphological operations (like erode and dilate or open and close) on images.

This plugin simulates color blindness. 
It is based on http://quarkphysics.ca/phys1/light/u-light.htm

This ImageJ plugin segments the image in classes by thresholding. It uses the same algorithm found in Otsu Thresholding, but was adapted to output more than 2 classes out of the process.