Software for counting fly eggs
ImageJ is a multi platform piece of software that has a cell counter module that might be of some use, and hey its free! Its easy to use and so ludicrously crude that it is very  versatile. I remember using it in undergrad to count cells under the microscope automatically after a few image contrast tweaks. I don't see why this couldn't be reapplied to count eggs.

Download: http://rsb.info.nih.gov/ij/download.html

Cell Counter documentation: http://imagej.nih.gov/ij/plugins/cell-counter.html