Metafilter. 5 dollar one time fee, actively moderated intelligent conversation about the best stuff on the internet. An ask question section that's quora without people trying to market themselves, and more. The 5 dollar fee (plus occasional donations from users who care) doesn't just pay for the site, it keeps out a ton of BS from spammers.

Hubski. An intelligent community that is designed in a novel way where spam is pretty much impossible. Each user follows other users, tags, and domains that they like, and can block tags, users, and domains that they don't want to see. When you "upvote" a post, you really are sharing it to your followers. Your feed is composed of posts to tags, users, and domains that you have followed. I really like it and want it to grow.

https://hubski.com

I occasionally stop by the Bootstrapped.FM forums, which seems to be the spiritual successor to the old Joel On Software forums. (Excellent podcast as well.)

http://discuss.bootstrapped.fm

Lobste.rs

http://www.theserverside.com/

http://lambda-the-ultimate.org/

Various sub-reddits... /r/machinelearning, /r/artificial, /r/semanticweb, /r/libertarian, /r/guns, /r/metal, etc.

QUORA but is next to impossible to write answers. I write a 500 word post with top grammar and spelling and the bot just deletes it for "spelling".

FORUM.WATMM.COM which is a forum for ambient electronica.

FORUM.BODYBUILDING.COM for the Misc for the l0lz

/r/rational - awesome subreddit about rational fiction. People and discussion are just as interesting and intelligent as on Hacker News.

Also LessWrong, though it's pretty quiet recently.