1. Sort comments by best, not top. Always.

2. Because programming is still a pretty big subreddit, I believe it's part of the default set: unlogged users and users creating an account will get prog as part of their default subreddit subscriptions. This brings "unwarranted attention" to the subreddit until the uninterested user realizes he can unsubscribe from prog. Things are getting better there as other subreddits have taken over as the juggernauts and are being ruined instead (gaming has 660k members, pics, funny and reddit.com have 850k)

/r/programming is the oldest subreddit and, IMO, has fallen the farthest in terms of quality of posts and comments. I have also become fed up with the banality of the main site at this point, but it's still pretty cool for niche interests like, e.g., /r/Minecraft.

It's no secret that the Programming subreddit has gone downhill in the past couple years. Plus, when a post gets popular, it gains the attention of the general audience, who often view /r/all.

Another good subreddit is /r/todayilearned

> it gains the attention of the general audience, who often view /r/all.

It's not that they view /r/all, it's that they have not customized their front page, so they get the default set of subreddits, which I believe is simply the subreddits with the most members.

I think it's the subreddits with the most members, except that mods can set their subreddits to not be on the default front page.

Try sorting comments by "best" instead of "top". It's not a complete fix, but it's an improvement.