It really depends on the type of agent you're dealing with.
The 'smooth operator' talky type is gonna need different challenges than the intellectual analyst type. However, the Agent skill tables do tend toward a fairly wide base of skills.
Almost any crime story can be adapted to Agents... stories that take a little Streetwise, a little Diplo, a little Computer, a little Gun Combat /Brawling. Without getting TOO deep into the Cold War thriller genre, the first three or four Tom Clancy 'Jack Ryan' novels would be good inspirations.