TL;DR: just read the bolded stuff...and resist the "TL;DR" impulse on meta!
If I was the most noteworthy one to suggest reflecting on it all, I'm very glad I did! I'm loving all the discussion here so far, and I'm probably running low on votes for the day as a result.
My point wasn't that we have any lack of strategy for handling single-user problems (not saying that's what you said, or that you would say that I'm saying that's what you said, and so on). I'm reasonably content with how it all went down in the end, though we may not have seen the end yet...My main concern was that I saw reason to sympathize with our friend "in the penalty box" (who has probably downvoted this very answer since returning, judging by a now-deleted comment), not just the mods and the mob (to which I belonged, so I mean "mob" in a sympathetic way too).
IMO, many of the problem actions resulted from good intentions that were expressed in dissenting ways with a majority that hasn't fully nailed down its policy preferences on a lot of things, or sufficiently addressed a number of valid concerns with policies as they are. A lot of valuable meta-questions have already been linked here that, ideally speaking, all of us would do well to visit, consider, and help resolve...but I don't know that I'm even going to put the necessary time into that myself. To some extent, we've all got more to bite off here than we can chew, mods included (that's one of the problems), and I don't know of anyone who's getting paid to dig in. We've all got to decide for ourselves how much we can afford to give, based partly on what we get out of the site (both for ourselves personally and for the causes we support). It's a labor of love, so it's wise to focus on improving what we love about the site and follow our own individual visions of what's going to keep people like ourselves coming back for more.
With what time and energy we can give, we should all decide largely for ourselves what we think will best add to what we and others like us can get out of the site. I hope that comes across as more than an empty platitude. I think it implies that we've got to respect the democratic process, keep the larger community's interests in mind, and do our best to serve them in ways that represent ourselves personally too. The democratic process takes time, doesn't always go our way, and works best when everyone gives everyone else a fair chance at changing minds and policy. These principles we all need to accept (FWIW, I'm sure most of us here have), because nothing much is going to really change them.
Nonetheless, sometimes being a radical, strident dissident is the most effective way to make a difference, but it comes with many costs and dangers. When users take that approach, I hope they'll consider the tradeoffs involved, and still be heard and respected by the rest of us even if they fail to return these good deeds. Failing that, I think we've seen that our mods will do what they need to do when they've got the right reasons and had enough time to deliberate on the right resolution. We've also demonstrated here that we'll do our part to support them and make the most of the situation, so for the most part, we're already doing the best we can, IMHO. Even dissidents and deviants do their part (our part? I sometimes feel like one myself), if only to round things out and help motivate the rest of the community to set its boundaries by testing them. I'm just as new as the other one who made all these waves, so I'm still having fun making some of my own. I'll have to settle into the flow sooner or later too, but in the meantime, I'm grateful to have both a voice and an ear for this open-minded dialogue with the existing community, and I hope the other will appreciate it all too.
Clearly, we have some rules and some limits. Yet it's also clear enough that we could use more clearly defined rules, and stand to be more knowledgeable individually about them, so that we can all co-moderate like SE intends. Know when to flag and do it sooner is a good tip, but I also try to add comments for the benefit of the user whose action I flag, to help communicate the concern regardless of what the mod does with it, preferably in a way that teaches the user how to avoid the problem in the future. When users don't listen or provide a coherent counterargument, I run out of patience for this, and just flag 'em and let the mods sort 'em out...but as @JeromyAnglim's answer implies, this shouldn't be our first reaction to a new user, even if he or she is just raising a tired old problem. Give each person a chance to hear you, even if others have already voiced the same concerns as you. Don't let people think that @ArtemKaznatcheev and I are "bullying" them just because we've already said what you think—it still helps to add your voice, not just your vote.
Certainly don't self-censor too much either. Respectful tone, constructive criticism, and care to avoid unintended offensive implications are all important, but none of this requires consensus. It's good to express dissent if it leads to systemic improvements, and the likelihood of this happening ought to inform the choice of whether to bother, but it's tough to estimate, because it's never just up to one of us. Every change takes a group, but every group needs a leader, so if you think you've got a cause worth leading, go for it. Don't be a groupthinker, be a leader. At the same time, know when to quit if you've got no support, and don't take too many causes on by yourself.
One of the benefits of paying more attention to meta-questions is that it builds the sense of where we agree and disagree, and on what issues. It's a great place to make a stand and lead the way (or try to, anyway), but paying attention to how others are doing so and figuring out how you feel about their causes is also a great way to reduce the need to act alone, and to mitigate the feeling of being singled out when these issues come up on the main site. Sometimes the gentlest and most persuasive way to point someone in the right direction is to link the relevant meta-question where a near-consensus has been reached; this is also a powerful way to deflect a critique, as I'd like to think I've demonstrated in one of my early comment contests (see also our most recent). In any case, visiting and linking meta-questions is a good opportunity to help define our rules by voting, commenting, and answering here.
As I've said, we've all got more opinions and knowledge to contribute than we have time we can afford to spend contributing them. I've spent a lot of time on this answer like I do on many, and I know they all take time to read, so I hope I've been succinct enough here in sharing my own opinions. I'll suppress the urge to scrounge up a long list of pet issues of my own to add to those linked here; @StevenJeuris' list addresses the OP pretty solidly already in that regard. The one issue I do feel is worth adding to the list is one that I think reflects some of the good intentions that went awry recently:
This question is currently +10, and has one disputable (+3/-1) answer that hardly settles the issue. That being: can't we do anything for the individuals who need help? We've already got clear limits on what we want to do with self-help questions (see also), and a good set of General strategies for converting self-help into a useful general question for this site, but what about the inquirer? I think this is where I sympathized most: I wanted to do more too, even though I knew I couldn't. In the same spirit as above, we'd do better by our self-help seekers if we can make our critical response more constructive for their purposes too, and if we can all do this together by collaborating on a meta-question that we can link to, that seems optimal to me.
I've taken a moment while writing this to Google up some contributions of my own, so I'll go do my part in a minute. Follow suit if you like, let me know what you think there or here, or just keep doing whatever else floats your boat. All activity is at least partly good as far as I'm concerned; we mostly need as much as we can get. If most of this answer ultimately boils down to a general cheerleading sort of message, I'm all right with that, because above all else, I want to help this site continue to grow into whatever emergent shape it will, given the lifeblood to grow: activity! (I'm oversimplifying the "state of the union" a bit here.)
However, existential psychologists make odd cheerleaders. As such, let me leave a little twist on that message: don't get complacent. We must do as much as we want to, not more, lest we lose the love for it. Thus we must know our limits, live up to them, and respect them, but also remember what we leave undone, and not hesitate to care about that too. That is the anguish of authenticity in the existentialist sense as I understand it. That is what will keep us coming back to finish the unfinishable.