As I understand it, comments should be used to ask questions about the puzzle or the solutions, but not for a "Thank You" note. Sometimes people are very responsive and provide extensive information. There is no information or question I could add, but I would like to thank that person for their quick response and/or effort. There is always a possible +1 to the puzzle, solution, or comment but sometimes I would like to say more.
I am currently experimenting with a new method. I add a Thank You note in the comment, then some time later delete it. This way the person (perhaps) sees their well-deserved Thank You, but the comment does not stay around to pollute the comment chain.
Is this an abuse of the comment system? Is there a better way to express gratitude? Ideally, there should be a thank you button which you may send more than once - then again, I often have a problem adding features to otherwise good software.