/r/science and /r/programming aren't bad
After that you should just check out niche communities and see if they've been taken over by trolls. So far /r/motorcycles, /r/ultralight, /r/camping etc have been fine, as opposed to the many iterations of /r/onebag which generally suffer from power-grabbing moderation.
I'd also like to hear about people's favorite subreddits in terms of comment quality, as I'd happily read a passionate and informative stance on something I'm usually not interested in compared to what I read on /r/politics.
Edit: I meant to use it as an example -- I'm actually interested in any type of subreddit, I meant to explain! So thank you for the suggestions and I'll definitely check them out :)
/r/christianity usually has fairly high quality comments and conversations among Christians and non-Christians.
/r/netsec has high quality posts and comments.
/r/hockeyplayers has a very helpful community but probably not of interest if you're not a hockey player.
/r/goodyearwelt has awesome reviews and information about high quality footwear
/r/malefashionadvice is one of the better run larger subreddits that has writers from major publications that post and comment
/r/askhistorians is very heavily moderated which means a lot of the most interesting questions remain unanswered for a long time, but the answers that are provided are very well thought out and sourced
/r/asksocialscience is similar to /r/askhistorians just different content
Granted it's center-left most of the time (from a US perspective anyhow - as a European it is at best centrist) but that's more a function of a reaction to the current climate than anything else.
So I guess I'd ask: "what kind of comments are you looking for?" because outside of the science communities you're not going to find better discussion threads.
For instance, you get one article about Trump's nickname for Sessions being Mr. McGhee. The comments decide this is bad. Then you read the comments on other stories and people are gleefully calling him a racist elf.
That's just pointless and is a disincentive to visiting. But I keep returning to the subreddit because of how helpful it is in keeping up with the Russia stuff and because of the rarer insightful comments that give reasonable perspectives you will never hear a major publication speculate on.
r/holdmyredbull - extreme sports cousin of "hold my beer". Other fun ones in this circle include "hold my juice box" and "hold my fries". I tend to think of watching someone go skydiving without their own parachute as universally interesting, ymmv.
r/AskReddit - Good survey of the current human experience, usually leave here with a feeling that your questions about the world and lives of other people aren't as unique as you though. Sometimes it's banal/off topic, though.
r/ELI5 - "Explain like I'm 5" usually contains layman's questions about science, maths, history, and other sometimes unapproachable with great responses from people who know their stuff. Almost always leave here with something new to think/talk about.
r/ProgrammerHumor - I'm a programmer, but even some of my non-programmer friends can enjoy the jokes over here.
If you're into woodworking, take a look at r/woodworking
r/hiking if you like hiking
r/campinggear for gear
r/baking if you like baking
etc. Just do a search for your hobbies and see what subreddits show up.
/r/askhistorians
/r/apple
I am forgetting a few more.
Good link content however.