I recently thought about the Back In Black arc in Amazing Spider-Man, specifically the sequence when Spider-Man has arrived at the prison and confronted the Kingpin, who hired the assassin that shot Aunt May. The part that was sticking with me was after the Kingpin has blah-blah about how all these killers and arsonists in the prison have 1 person they all look down on: the chump, meaning Peter Parker. Spider-Man responds by punching Fisk repeatedly, but without saying a word. After a bit of this, Fisk demands of Spider-Man something to the effect of "Well, you said you were here to kill me, so are you going to do it or not?" At this point we get a lovely 4-panel sequence by Ron Garney, where Spider-Man responds 'I'm not here to kill you', removes his mask and the upper half of his costume, drops them to the floor, and then Peter Parker says 'I am'. The next page is Peter charging towards Fisk*. There's something about that sequence I've always found interesting (I even alluded to it when I reviewed the issue last year), but I never got around to discussing it. Now's as good a time as any though. So first, here's the page in question. Sorry it's not too large, it was the biggest version I could find online. Discussion continues below.
So I think it's clearly meant to be significant that he removes the mask to settle this, even though everyone present already knew who he was under the mask. Spider-Man has often been Peter's way of escaping his problems. How many times over the years has he gone out web-slinging in an attempt to clear his head? How many times has he been moping about some problem in his life, only to see a crime in progress and actually be relieved that he has something to do? Peter Parker, at least occasionally, uses Spider-Man (and the responsibility he feels to use his powers to help others) as a way to avoid dealing with his problems. If Gwen Stacy hates Spider-Man, and is angry at Peter for trying to defend him(self), punching out the Gibbon doesn't solve that, but it does let him ignore the problem for awhile.
Besides that, Peter also uses Spider-Man as a way of dealing with things that bug him in his life, in ways Parker can't. Peter Parker finds himself flailing with the ladies? Well, Spider-Man's never at a loss for a clever line. Flash Thompson picking on him? If Spider-Man shows up, you can be sure Flash will be the first one in line to shower him with love and respect. Jameson using your photos of Spidey saving an old lady to portray him as an enemy of the elderly? Sneak into his office, leave him a little webbing surprise on his chair. He can do all those things because no one knows who is really doing it, so he gets his kicks without facing any responsibility for it**.
Here though, Peter hasn't opted for that. Partially because it doesn't matter (as I said, everyone already knows it's Peter Parker under the mask). Partially because it was Peter that Fisk struck at, not Spider-Man. Most of the time, Spider-Man fights people who want to kill Spider-Man, so it's only proper he fight them as Spider-Man. They didn't know who was under the mask, and he was just fine keeping it that way. It's the guy in the mask with the webbing and the jokes that vexes them, not the nerdy photographer. But this is a case where the villain has aimed at that nerdy (former) photographer, and so he's decided that's who has to respond. It's not the first time I've seen this response, either.
At the end of the Clone Saga, Spider-Man #75, as Spider-Man fights the Green Goblin, he removes both their masks and says it's about two men, named Osborn and Parker. And it is. They're fighting on top of the Daily Bugle, and Norman had tricked many people there to kill them, all because they were close to Peter (Ben Reilly saved them). Plus, Norman returned because he blames Peter for Harry's death, and since Norman knows, it is Peter he blames, not Spider-Man. I imagine on some level, Peter blames Norman for Harry's death, too. And of course, there was the specter of Gwen Stacy. It was about two guys who feel the other has hurt them, as a person, not as a costumed entity, and so it's proper that they end the fight as people.
Which brings us back around to Amazing Spider-Man #542. Fisk attacked Peter Parker. If he'd wished, he could have ordered the killer to go to the address they were given, then follow Spider-Man and try to eliminate him during the giant skirmish that in Civil War #7. He didn't. He wanted it so that even if only one of Peter, MJ, or May was hit, the other two would be present to see it, have it burned into their brains forever, the sight, the sound of that moment, even if "forever" was only the time needed for the sniper to pull the trigger again. Going after a man's loved ones demands that the man respond. It's especially interesting in light of the theme JMS played with through his run, about where Peter's powers come from, and the battles where Peter makes some internal distinction between the Spider and the Man, such as the conflict with Shathra. When he lost control in that battle, Shathra said that the man was gone, only the spider remained, which was what she wanted, since the "spider" was what would be fed to her children. But here with the Kingpin, Peter is completely under control, even though the hurt inflicted on his loved ones is even worse than what Shathra did***.
Nope, Peter isn't blindly reacting here, he's thought out what he's going to do to Fisk, and he executes that plan exactly the way he wanted. The Spider might have killed Fisk for encroaching on its territory, but the Man chooses instead to destroy Kingpin's most valued possession, by making him look weak in front of all these scumbag prisoners, costing Fisk their fear and respect. He leaves Fisk alive, but crippled, and with the knowledge that at the moment Aunt May dies, Peter will come back, and then, Fisk will die. And there's absolutely nothing he can do to stop it. That may even be the Spider showing through a little, striking at his prey, then sitting back and waiting until it can't fight to finish the job****.
The one thing I think would have made the story better is if Peter hadn't revealed his identity to the world. Rather, Fisk found out some other way, ala Born Again. Then the act of removing his mask in front of all these criminals would have real impact, because while they might not know his name*****, he's willingly showed them his face. Because he doesn't care, this has to be handled this way, and besides, he intends to make it very clear why they shouldn't try what the Kingpin did. If Fisk hadn't already mentioned his name, you could have a scene where Fisk does so as Spider-Man goes to leave, and the cons all act as though they heard nothing, simply figuring it isn't information they want to know anymore. Wasn't the hand JMS was dealt, though, so I feel he and Garney did pretty well with what they had.
* Preparing to deal a monumental and humiliating beatdown on Fisk.
** Except for the possibility that his prank puts Jonah is a bad mood, which he takes out on Peter the next day at work.
*** For those not familiar with that story, Shathra assumes human form, and goes on TV claiming to be Spider-Man's mistress. She claims that he looks freaky, and has odd sexual interests, and that of course he's married, but he probably just uses the wife to feel better about himself. Both MJ and May see this report and get rocked by it - especially MJ - and it drives Peter berserk, to the point where's he basically an animal when he attacks.
**** That's a common tactic amongst sharks, for example. Get one good bite, then hang back until the prey bleeds to death, so that it doesn't risk being injured when it tries to feed. Venomous snakes exhibit similar tendencies, so I can imagine certain spiders might as well.
***** I can't recall whether Fisk uses his name in the preamble before the real fight, and if they didn't already know, Fisk might not use it anyway, preferring to keep that little tidbit to himself.