“Great” and “Great Effort” are affirmative replies.
They are typically written after the professor has read the entire paper. In using these comments, the professor calls attention to how you consciously have written the paper. Yes, every student writes with some level of consciousness just as everyone who is not a student does.
However, in this case, the professor believes your paper reflects a certain level of alertness and careful attention to detail. The quality of your paper is much more than ordinary and it is one level up from “good.” For example, a professor might write “good” in the margins to highlight a certain paragraph or call attention to the soundness of your expression within a particular area of the paragraph. The professor will rarely use “great” in the margins.
“Great” is written typically at the top left side of your paper, after the finished read. In this respect, the professor believes your paper has been a delightful and pleasant read.