It's informal and not perfectly grammatical, and it has two possible interpretations. In either case, "done right" means "done properly" or "done well." It could mean: a) "That was the best course in the department and it was done right." High praise. b) "That was the best course in the department when it was done right." Qualified praise. Depending on what semester and who was teaching it and how it was taught, sometimes it was the best course in the department.

That was the best course in the department, done right!" X That was the best course in the department if done right!" > This is okay. If done right > if it is correctly done.