I have been told that I have a habit of saying "good question" a lot of the time when people ask me questions. I can't deny the allegations; now that it's been pointed out to me I catch my self doing it very often. The thing is, I don't know exactly why I say it. It's not an automatic response, and I don't say it for every question for the same reason I don't say "good table" every time I see a table. It usually doesn't merit comment even if it is a very good table.
I think the habit formed for me around teaching other engineers about code. In my experience, the longer you stay at a software company, the larger the percentage of your time spent on explaining the intricacies of your barely-clinging-together code to newer hires, so there have been a few periods of my life where a lot of my time was spent explaining insane contraptions to people who were, on the whole, very good at understanding insane contraptions. I think in this context, I say "that's a good question" to mean "that this question occurred to you demonstrates that you're making correct intuitions about the topic".
There's also a case where the phrasing of a particular question will make me form a new intuition about the topic and I'll say it slightly differently, "now that's a good question". I'll then answer if I can and explain why I thought it was a good question, so we can both co-verify the idea.
Looking back, I think this has been helpful in the specific case where I have a lot of domain-specific knowledge and the person I'm speaking with doesn't. It's good for catching misunderstandings early in a very complicated environment where misunderstandings are common and difficult to detect sometimes. I think the practice is helpful in peer discussions too, particularly the explaining of why the question is good. It's sometimes led to disagreements where I ultimately came around to agreeing that the question wasn't so good after all (i.e. the intuition that the question relied on was incorrect).
Where I think it gets annoying is in casual conversation, especially at the frequency that I unconsciously do it. What's odd is that, while I do it a lot, the reasons I say it in casual conversation are much less clear than my reasons in technical conversation. The nearest I can tell it's "I had a new idea because of that question" which, in casual conversation, happens all the time. Compared to technical knowledge transmission it's almost all new. So it became a semi-automated response that was firing, frequently, without my ever noticing how often it happened.
So to my question: What makes you say a question is good? do you say it out loud or do you just think it? Or do you think it? Does the idea of a question's "goodness" even make sense to you? I'm not sure it does to me.
Bonus question: What makes you say "good point"?
If someone identifies flaws or associations that have not yet been considered, to expand the perspective - especially if it’s phrased as a question, even a rhetorical one.