I use it as a "like" button à la facebook. I'll never leave kudos on a story I didn't much care for, and certainly not on a story I outright disliked. I usually leave kudos (rather than a comment) if I'm pressed for time, low-energy, or don't have any thoughts about the story that could be communicated better than "I REALLY ENJOYED THIS."

I'm more likely to comment on stories at livejournal or dreamwidth, simply because I'm more used to the journal environment, but I've left comments on stories at AO3.