Counting colonies on agar plates is a widely used method in microbiology. OpenCFU is a free software that should facilitate (and render more reproducible) the enumeration of colony forming unit (CFU). You can simply run the program on your computer and input pictures of plated bacterial colonies (or other cells).
I am happy to announce the availability of OpenCFU 3.8-BETA. This version is a foretaste of the future stable version 4.0 which comes with many improvements. Take a look at the video to discover the new features!