AFM and STM 3rd Party Software for Image Analysis

Image SXM (Mac) A version of NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Seems to be able to open lots of file formats, but only works on MAC. A paper about Image SXM Software for SPM Paper
Gwyddion (PC & Mac) Freely available, open source software for manipulation of SPM files; supports very many formats, contains many analysis tools. Available for Linux, Windows and MAC OS. Frequently updated
WSxM Program Freely available software that supports many SPM file formats; and has many analysis tools. It was developed by an AFM manufacturer for use with their instrument, but also supports very many other file formats. Unlike many third party programs, has good support for force curves as well. Frequently updated.
True Map True Map is an analysis and display program. TrueSurf is a surface roughness analysis program. These are extensions of profiler software packages, now offering some AFM format support. Commercial software, a licencse must be bought for extended use.
Scanning Probe Image Processor (Commercial)
Software for SPM
List of Software for SPM