Been using reddit for about 6 years, some of the smaller subs are amazing and I think it comes down to two major things, excellent moderation and community below a certain size (usually).
I've thought about this for a while on and off and I'm not sure how you could scale that up in terms of moderation, some of the defaults do well while others are just a wasteground (I've also wondered if that is partially intentional in the sense of give the idiots a subreddit as a decoy).
I like reddit but it has it's shares of trolls and typical online negativity (which I actually dislike far more than the trolls they at least are easily spotted, the constant negativity wears you down).
/r/AskHistorians is one of my favorites. Mods are insanely hawkish about the rules which slightly turned me off when I first subscribed. But after a few months it started to make sense and the quality of contributions is superbly high.
I really enjoy /r/photography, the quality of discourse is high and there are very little nastiness. The mod team is also highly active and engages members - weekly discussions along directed topics, weekly writeups/discussions about famous works/photographers, etc.
IMO subreddits like it are evidence that the Reddit macro model has been, and will continue to be a failure. The community is at its best when tone is actively directed by a dedicated mod team, and abusive behavior actively policed, in distinct contrast to the relative free-for-all that are the default subreddits.
Reddit's admins make a lot of noise about believing in the hands-off approach ("every man is responsible for his own soul"), but ultimately the hands-on approach create higher-quality communities (even at scale: see /r/iama) and curbs the abuse that has made the default subreddits complete intellectual wastelands. Not only that, Reddit itself has not been consistent on being hands-off, what with the banning of subreddits and whatnot.
Side shoutout to /r/movies - always good discussions. Things get more animated and sometimes less civil than /r/photography but the mod team does a good job keeping things from exploding.
I find these subs to be on topic, relatively positive, often receptive to the new and uninitiated, providing a wealth of FAQ/just starting out information and have interesting weekly events.
I especially enjoy the header with album release dates in hiphopheads, and there are a number of cool weekly events in frugalmalefashion (and its more expensive brother subreddit, http://reddit.com/r/malefashionadvice).
As with any sufficiently large group, you'll find groupthink. However, I've found that many smaller subreddits are more receptive of self-criticism when it gets too bad.
Seriously. When I joined reddit there wasn't an active hip-hop board (which was the only major interest I had that reddit didn't have an active community for).
So I thought I'd take it into my own hands. Started posting content, inviting users who I thought would be interested, and almost 5 years later, turned into what it is today.
As a mod of /r/javascript (for about 6 months now), I'm flattered. The sub really is easy to mod though; yes, we get a couple off-topic & spammy posts every once in awhile, but by-and-large, the JS community there runs itself really well.
Some of the communities around mental illness offer very caring communities. Obviously I think it is mostly because of very strict rules/admins. It is special to have an anonymous place to vent and have people understand you without trolling.
Most of the sports subreddits are pretty awesome. /r/cfb is my favorite, but /r/baseball, /r/hockey, and /r/fantasyfootball are all quite good as well. /r/nfl is probably the flagship sports subreddit, but it has been a little rough lately with the community and mods having some conflicts about the direction of the subreddit.
Lately I have had a sad feeling that r/nfl has reached an inflection point where it is quickly degrading into just another large subreddit. The firestorm surrounding the NFL's domestic violence issues this season seems to have had permanent effects on r/nfl.
/r/nba is also awesome, along with literally every individual NFL and NBA team sub I have ever visited. Most are quick to ban opposing team fans for anything resembling trolling though. Tread lightly.
I really find the various city subreddits to be quite useful, such as /r/chicago and /r/sanfrancisco, for local news, discussions and events. I've learned about many interesting activities this way and it also helps you stay in touch with the local culture when you're away.
/r/Fantasy (63,661 readers) is great. And sometimes it feels like half of it's users are (somewhat) well-known writers ;)
Seems to need less moderation than other subs of this size.
/r/Polandball (101,218 readers) is heavily moderated (important considering the jokes there easily invite real racism)
/r/ASoIAF (166,200 readers) and /r/gallifrey (38,643 readers) are examples of very good TV/book subreddits (A Song of Ice and Fire aka. Game of Thrones and Dr. Who). the mods work hard to keep the quality up but have the advantage of the "mainstream" subs /r/gameofthrones and /r/doctorwho which both gather most low-effort posts.
On the fence about categorizing /r/clojure and /r/ece as good. They're not awful, but they need more traffic to be "good". /r/ece is almost an informal 24x7 AMA for EE and CE and the rules are constantly being broken but not necessarily in a bad way (if that makes sense?)
There are subreddits I find interesting to read but probably miss the categorization of "good" by being rather subjective based on your personal opinions of the subject matter.
Here's a plug for http://reddit.com/r/languagelearning. Most of the language related subreddits tend to be pretty good. There are also a couple decent computer science subreddits, but you can explore those yourself. http://reddit.com/r/wicked_edge will help you learn to be a better shaver and actually enjoy it! Those are a couple I like.
They'll be very person specific but sure I like these (some are less than perfect).
/r/futuresynth (no one comments but the stuff is great,
nearly perfect ;))
/r/ada
/r/embedded
/r/raspberry_pi
/r/bicycling
/r/programming
/r/linux
/r/nottheonion
There are some subs I try to like /r/minimalism (which on any given day is either "I have nothing...but these apple products" or "Two arms..one too many?") and /r/zen which is mostly people arguing vehemently about what zen is (which is both ironic and often hilarious).
Every time this comes people complain and whine that it would ruin the sub. I'm on the side that posting images should be banned. In subs I've seen this implemented it's helped content a lot.
If you're into sports, /r/cfb and /r/nba are two excellent subreddits. /r/nfl is pretty good, but there's always some fights with the mods over what posts get removed, merged, etc. Nothing too bad, but there's a little more drama than the former two subreddits.
/r/motorcycles and /r/guns are good as well if you're into that sort of thing -- /r/guns is especially funny on the weekends ;)
I've thought about this for a while on and off and I'm not sure how you could scale that up in terms of moderation, some of the defaults do well while others are just a wasteground (I've also wondered if that is partially intentional in the sense of give the idiots a subreddit as a decoy).
I like reddit but it has it's shares of trolls and typical online negativity (which I actually dislike far more than the trolls they at least are easily spotted, the constant negativity wears you down).