I've imaged graphene planes in nanotubes in grad school, but never an individual atom... Either our microscopes weren't that tightly set up (Read: old and less precise), or I wasn't good/patient enough to do it. Now, they just won't let me play in the lab any more.
Electron microscopes are incredibly powerful and amazing tools. SEM's are where we get all those really nifty pictures of mites and bug feet (and etc...), but TEM's are really the ones for examining microstructures on the atomic level. That's where you get pictures of atomic planes, dislocations, inclusions, spot defects, etc, etc, etc. and then you've got STEM's (not scanning tunneling, but scanning transmission electron microscopes... same acronym for two different tools) which are REALLY cool.
The real challenge, however, isn't so much of using the microscope to obtain the image (though that requires a significant amount of skill), but rather the actual preparation of the sample such that you can image the area or feature of interest... for most of us (IMHO), getting that perfect micrograph is as much a game of luck and numbers as it is skill with the microscope!
in my opinion, the most impressive images are the ones where the researchers have captured some sort of reaction at the molecular/atomic level in-situ... that's just awesome to see!