Well, first of all I am not good... saying things xD as @Coati said, sometimes you just don't know what to reply.
I do put a like on every comment we receive though, or almost every. Then if I can answer something on it or if I have anything to add to it, I do.
If there is a comment "good comic, I like it", I most definitely will write that I am glad or a thank you. If a reader notice a detail, I will praise them for that. If they have a question I can answer without spoiling - sure. If it's a comment with reference, I will answer with the reference in mind or ask something, because I do not understand that reference. If they write something I find funny or original, or even when I like their name or something, I will answer =) Even something like this sometimes
Personally, if I write a comment, I do not expect the author to answer. I just express my admiration for their work. If they answer - great, if they don't - well, that's not what I was even going for. Some of them have thousand comments a day, I think most of us understand that they are the working people with the same 24 hours, and not the robots who are sitting there writing "thank you" under every comment.
In the end, answer to comments you are comfortable with answering to