Micro Manager
Micro manager is a free, open source software package you
can use to control your microscope and cameras. It's a
brilliant idea.
OsIRIX
Is a wonderful, open source piece of software for looking
at 3D and 4D image sets. While the original users were
folks looking at medical imaging sets, this has become an
increasingly useful tool for those of us that collect
stacks of images from living cells.