http://www.reddit.com/r/somethingimade/
http://www.reddit.com/r/longtext/
http://www.reddit.com/r/programming/
http://www.reddit.com/r/PhilosophyofScience/
http://www.reddit.com/r/cogsci/
http://www.reddit.com/r/startups/
http://www.reddit.com/r/compsci/
http://www.reddit.com/r/SomebodyMakeThis/
http://www.reddit.com/r/browsers/
http://www.reddit.com/r/gamedev/
http://www.reddit.com/r/shamelessplug/
http://www.reddit.com/r/Freethought/
Not all of these subreddits are busy but it doesn't matter. I have over 50 hand-selected subreddits and even though I removed all of the popular subreddits (reddit.com, politics, pics etc.), I always see very interesting articles. And the number of comments in each article is usually between 10-50, kinda like HN.
If any of the subreddit starts to get too popular and mainstream, usually 2-3 new subreddits popup that are more specific and interesting. Once a week I spend a few minutes looking for new interesting subreddits. http://www.reddit.com/r/newreddits/ helps with that too.
If you really want to start a web-community, just ask for mod permissions on a few subreddits that interest you. I'd much rather click once to join a subreddit and view its articles during my regular reddit browsing than go to whole another site. I wish HN was available as a subreddit. I would never have to go to another news site.