I try to provide answer to every comment, but just because most of those comments on my articles deserve answering.
I really can't find comments that say just: "great article", but those are mostly some new comments, and personal insights into the subjects I write about. I find it polite to thank for new information provided by my readers, and to even update some information in article that I think would make greater impact if put into the answer to one specific reader than put in the article body.
I also like when people on other sites, blogs and articles answer to my comments, because it is way of communication, and making bounds between the writer and his readers. In this modern world, it would be equivalent to not saying back "hi" in the street.
Of course this works for me who have few articles. It is completely understandable not to answer every comment for those who have 100s f articles around the internet.
This is just my humble opinion.