Computer Networks: Graphs model intuitively model computer networks and the Internet. Often nodes will represent end-systems or routers, while edges represent connections between these systems.
Data Structures: Any data structure that makes use of pointers to link data together is making use of a graph of some kind. This includes tree structures and linked lists which are used all the time.
Pathing and Maps: Trying to find shortest or longest paths from some location to a destination makes use of graphs. This can include pathing like you see in an application like Google maps, or calculating paths for AI characters to take in a video game, and many other similar problems.
Constraint Satisfaction: A common problem in AI is to find some goal that satisfies a list of constraints. For example, for a University to set it's course schedules, it needs to make sure that certain courses don't conflict, that a professor isn't teaching two courses at the same time, that the lectures occur during certain timeslots, and so on. Constraint satisfaction problems like this are often modeled and solved using graphs.
Molecules: Graphs can be used to model atoms and molecules for studying their interaction and structure among other things.