It is quite literal. It means the person thinks it is a good question. It usually means that they think that the question demonstrates insight and understanding of the topic.

Jim, as I understand it, your colleague is a student, and he often BEGINS a statement with the words "Good question." He is NOT responding to any actual question. This isn't any idiom or common usage in U.S. English. How does he follow this phrase? Does he follow it by stating a question of his own? Can you give us an actual example of his exact words? It isn't strange, but it isn't a standard way to open a sentence. This is just a guess: I think it's a _personal_ "turn of phrase" he uses himself. A lot of people have personal little speech habits of their own. It probably means something like "Pay attention" or "I think this is important, please listen." If you are close enough friends that your colleague says "Hi, Jim" to you when you see him, I think you should just ask him about it. I can _imagine_ a conversation like this, but it isn't a common or idiomatic thing to say. A: "I need to return my library books." B: "Good question: this is the day after Thanksgiving, is the library open today?" A: "Hmmm. I'm not sure. I'd better call." Someone else might have said "Ummm. Errr. This is the day after Thanksgiving, is the library open today?" Or "Actually, this is the day after Thanksgiving. Is the library open today?" It's just a kind of filler noise that means "I'm about to say something, please wait a second while I form the words in my mind."