The story this thread refers to is the perfect example: it was #1 with 200 upvotes after just a few hours. The link was then changed to a different domain that covered the topic in more depth, and the story was suddenly buried within a half hour--apparently by flagging. How was the first link so popular and the second link inappropriate for discussion when the topic was the same? Either some users are just very prejudiced against certain domains, or there are some users and/or organizations that have automated systems in place to detect certain domains or links and send alerts to bury them.
There have been enough times where I've witnessed completely factual and legitimate comments here that happened to criticize or even just question Mozilla, Rust, Ruby on Rails, NoSQL, or some other "revered" organization or technology get heavily voted down without justification.
Some of this may just arise naturally. Certain submissions may draw the attention of people directly involved with the given organization or technology. They may take it personally when the discussion touches on perfectly valid, yet perhaps painful, topics. They respond by downvoting these comments that are totally valid and raise some good points. Even if these people are not intentionally acting maliciously, this misvoting can still be quite harmful.
I'm not certain that there's a good way of dealing with this, however.
So sum it up, me and somebody named jsmthrowaway happened to point out some painful realities regarding the Rust programming language. The facts we brought up must have hurt the feelings of some within the Rust community (several prominent figures were involved with that discussion), and so numerous factual and perfectly legitimate comments of ours within that thread of discussion basically ended up censored.
Now, I personally don't care about karma, or whether people agree or disagree with opinions I express or facts that I may happen to point out. What I don't like, however, is seeing perfectly good content grayed out, regardless of who posted it. Censorship is always harmful.
These days, I find the grayed out comments more disruptive than beneficial. Many of them are perfectly valid content. Some of them often are quite insightful, in a way that some people probably find painful.
So instead of being comments that I feel comfortable ignoring, I usually find myself trying to read the grayed out ones even though they've been obscured and are harder to read. They're often the most worthwhile comments within a submission's discussion.
It isn't the only instance, of course. Mis-moderation is quite frequent here. Some of the discussion under this submission is a good example of that. I see I have once again been targeted by people who find it easier to downvote than to bother discussing the matter at hand like adults.
I wish that people here were more willing to discuss stuff that they might happen to disagree with, rather than engaging in censorship.
(I don't speak for the other topics, though.)
"That Daniel Gackle is the HN moderator" is the kind of factual detail you might want to know before developing very strong opinions about how the site is run.
Second, if you don't trust the site moderators, HN isn't going to be a pleasant place to spend time.
The story in question here had 200 upvotes when it was a link to an NSA story at Slate. The link was changed to the same, source NSA story at First Look and it was quickly flagged to oblivion. I think there're likely some monitoring scripts and flag alerts at play, not just NSA fatigue by actual users.
But many articles are flagged by users, don't assume that all the penalties/kills are dew to moderators actions.
If you submitted an NSA story and it fell off the front page, it was user flags that did it, not the penalty.