Is there an honors system in graduate schools?

At my university, you can graduate at the doctoral level "with distinction." This is the only honor we offer (aside from dissertation prizes) and it's entirely based on the dissertation, not on coursework.

We don't even calculate the GPA of our graduate students.

I think that it significantly depends on country and university, but, based on my kind of unfortunate experience, graduate schools very rarely use the Latin honors system (with the exception of the JD degree and, less frequent, some other degrees - see below for an example).

As a recent Ph.D. graduate with high GPA (3.94, which usually corresponds to summa cum laude), I was wondering the same thing, while updating my CV and resume. I have asked someone at my program's office, but the reply was that at our university the Latin honor system is used usually for undergraduate and, perhaps, for some medical degrees. The lady was polite and advised to inquire further at the program's office. However, after reading the corresponding Wikipedia article and browsing some graduation-related documents on my university's website, I have figured that further research is not worth spending my time, so I have just made sure that my CV and resume contain correct GPA numbers for all my degrees (it is not as practical as the Latin honors terms, since those terms can be used in other contexts beyond the one of CV or resume). I hope this is helpful.

NOTE. Here's the information on grading and academic honors at some of the top MBA programs: http://poetsandquants.com/2014/02/27/how-mbas-are-graded-at-top-schools/2. Note the total lack of graduation honors at Yale. Despite the existence of a variety of unique honors at some of the top schools, for the majority of the rest of graduate schools, the most common academic honor terms at the graduate level seem to be "with distinction" or similar, as mentioned by @RoboKaren.