Well, almost anything that is solid can be analysed by AFM!
Here is a short list of SOME samples, in no particular order:

• Polymers
• Metals
• Fibres: Hair, synthetic fibres, nanotubes
• Particles: micro-, nanoparticles, quantum dots
• Molecules covalently bound to a surface: e.g. self-assembled monolayers, and others
• Molecules that are NOT bound to a surface, e.g. nucleic acids, proteins, many others
• Minerals
• Langmuir-Blodgett films, Lipid bilayers
• Cells: Mammalian, Bacteria, Plant, etc.
• Viruses
• Ceramics
• Plant surfaces: e.g. leaves, fruit
• Paper

In short, if it has a surface, and it's solid, AFM can image it.
There has even been some work reported on gel and liquid surfaces.