See also: Reddit's "best" ranking for comments: http://www.redditblog.com/2009/10/reddits-new-comment-sortin...
What it doesn't address is the quality or relevance of the upvotes themselves. Spend much time on reddit and it's clear that there are a great many people who are voting on stories and content with little regard to its significance or truth.
As a measure of popularity or agreement, the metric is ... better than most. As an indicator of true quality it continues to inherit the faults of virtually all online moderation systems. Absent either creating a class of users who are considered "trusted moderators", or a means of finding agreement between a given reader's preferences and those of the raters indicated, that's pretty much a persistent issue. The better subreddits, in my opinion, address this through guidelines, posting policies, and very strict subreddit moderator policing: removing nonconformant or low-quality posts, banning individuals who troll or don't follow posting / commenting guidelines.
Even subreddit mods cannot change the voting on submissions or comments themselves (nor can they see who's voted on what), but they can influence what is visible within the sub -- editorial prerogative.
A moderator deleting someone's comment should be the last resort. It's irritating to spend 5 minutes writing a comment in a subreddit, press post, then see "the comment you're replying to no longer exists" because the moderator decided deleting a thread of 10 comments was more appropriate than taking some time to write a comment with their own opinion. It's also irritating when one's own comment with 4 upvotes is deleted while someone else's comment with 6 downvotes remains untouched although collapsed. This recently happened to me twice, a week apart, on a subreddit I'd been visiting intermittently for the last 4 yrs, and very occasionally commenting in, without any trouble.
> Even subreddit mods cannot change the voting on submissions
Perhaps this is the real reason a subreddit moderator deletes upvoted comments they don't agree with, while leaving downvoted ones. Downvoting and replying should be the means to control quality, with a moderator deleting a comment as the last resort.
The tune's a bit different in /r/economics, where while posts aren't deleted, there's a very strong bias toward economic orthodoxy, despite the many, many, many flaws it contains (full disclosure: my degree is in economics).
For my own subreddit, the focus is on intelligent discussion. I make no bones about deleting trolls, or even just vapid comments. I'm not looking to win any popularity contests.
And in some subs it is iust a lot easier to delete posts that are almost trolling than to allow a large angry thread to spawn. Often those are the same tedious meta topics, or very simple beginner topics, that have been covered very many times and which are not interesting but which are flamebaity.
But green is not reliably "new". It tends to be strongly correlated to newly created accounts, but I've seen weird behavior (like a child comment is marked green... whereas the comment thread was started by the same commenter in gray in the first place), which leads me to believe there's something subtler going on. I thus have no idea what the difference in color is supposed to indicate at all.