I resort to comments like that when I don't have another way of contacting the user. If it happens in a Show HN thread, it's probably that I want to ask if they've considered applying to YC with the project. People often underestimate what YC might be interested in. Open-source startups are a big part of what gets funded these days. I particularly love it when startups make it in to YC through HN—it's great for both YC and HN, and if a big success ever came out of it, it would easily fund HN for another century :)
If I post a please-email-me outside of a Show HN thread, it might be anything! but the most common reason is that I want to send them a repost invite for some cool article they posted long ago. Invited reposts make it into the second-chance pool (see https://news.ycombinator.com/pool and https://news.ycombinator.com/item?id=26998308).