In Amazing Spider-Man #541, page 17, the first panel shows Peter in regular clothes, swinging across the city on his way to confront the Kingpin. What caught my eye is that Garney only draws the outline of Peter, and then we a get a sort of psychedelic, watercolor looking thing within the outline. There are no other details within the outline, just colors: Reds and oranges near the feet, blues on the upper torso, getting lighter as you move towards the fingers and the head. It seems so odd, I figure it has to mean something. But what?
My intial thought was that the colors represent inner turmoil, Peter struggling either to bring his darker impulses under control, or to encourage them, knowing that if he really intends to do this, he has to fully embrace his rage. However, I think that for that the colors would need to be blending, swirling around each other more, to demonstrate the conflict. But as I noted, it's mostly reds at the feet, and blues at the head and arms, very little mixing. Perhaps most notable is that his head is more of a pale greenish-blue, whereas his chest (read: heart) is a darker blue. This could suggest either depression, or that if the blue implies anger (an odd choice, but maybe), in his mind, he has more doubts about what's he's planning, that the anger hasn't entirely clouded his judgement. But there's more to the panel than just Peter, so let's go broader.
Starting with the context. Peter has just finished giving Aunt May some of his blood, hoping his spider-strength will assist in recovery. That done, he's decided it's time to face down Wilson Fisk (without drinking any juice or having a cookie, no less). In the panel, Peter is upside-down, the city beneath him. To look at him right-side up, would force up to flip the book upside-down, but the city would still look more or less the same. It perhaps emphasizes just how things are going for Peter. In the past, Peter hid his Spider-Man identity from Aunt May, and his injuries, absences, and lateness caused her great stress, and periodic health problems. But now his identity is out in the open, known not just by her, but by everyone, and May still got hurt because of Spider-Man. For Peter, everything is falling apart (read: upside-down), but the results have wound up the same (the city looking normal whether you view it upside-down or normally). Peter's big decision has only fouled up his life, it hasn't really changed the world in any significant way.
The fact that even as Peter's life has changed so drastically, certain things still hold true (Peter being Spider-Man impairs a loved one's physical well-being), is further reflected in the illustration and coloring of the cityscape below. The buildings are drawn and colored normally, or consistent with how they had been drawn in the issue thus far. Perhaps it symbolizes the disconnect of Peter from the world beneath him, the society that's deemed him a criminal, the society that has said "No more vigilantes!", even as Peter is preparing to take a page out of the Frank Castle book of vigilanteism (that's not even a real word, is it?).
In the upper left corner of the panel is a text box, containing the second half of what Mary Jane is telling a nurse entering May's room. It says 'It's too late.' While this most obviously refers to Mary Jane having missed her last chance to talk Peter out of going after Kingpin (at least at this precise moment), it could also mean it's too late for Peter, in any number of ways. Going after Fisk now won't make Aunt May be uninjured, it's already happened. It may be too late for Peter to step back from the decision he's made to kill Fisk (we know it isn't, but roll with it).
There have also been several scenes of Peter swinging through the city in this story arc thus far. Maybe there's a pattern we can glean from those.
Amazing Spider-Man #539: On pages 5 and 6, Peter swings to the hospital, carrying Aunt May. He's in civilian clothes, fairly well-lit, as is May, until she passes out and her face falls into faint shadow (dark enough it's noticeable, but not dark enough to obscure any facial features). Peter's face is completely visible on page 5, on page 6 we get a shot of him from behind as he cries out 'May!' Perhaps at this point Peter still has hope that things will be OK?
On page 11, the last panel shows him below and from behind, as he swings away from MJ vowing to 'hurt someone'. Even though it's broad daylight (probably not a good idea for a wanted fugitive to be web-swinging at that time in Times Square), he's completely in shadow, an indication that the anger that was observed in panels 2 and 3 of page 7 (as he hears the doctor's commenting on May's condition) has taken a firm hold of him.
By page 15, he's looking for someone to tell him about the piece of the sniper scope he found. The anger is plain on his face in the first panel, as he's extremely well-lit, but by the third panel, he's moved past us, and once again we see his back in shadow. I'm not sure what to make of the first panel, unless it's mean to surprise us with a scene of Spider-Man going into action out of costume, with emotions that would normally be hidden, plainly displayed.
Amazing Spider-Man #540: Peter spends most of this issue in costume, and does all of his web-swinging while wearing the spandex. Interestingly though, a good portion of the issue takes place during the day, whereas #539 and #541 were predominantly at night. This is because shadows are rarely needed to convey anything about Spider-Man's emotional state. The fact that he's donned a costume he threw away because of how it bothered his wife (yeah JMS said it was for a different reason, but he doesn't know jack, so whatever). The fact that he's getting into a fight with a gunman in the middle of a train station. Forget that he's a fugitive and someone was probably calling the police, who would call SHIELD. He attacked this man, who Peter had to know would be armed, with people all around him. His facial expressions don't need to show us how he feels, because that kind of reckless action tells us enough about where his mind is. This is not about getting a killer off the streets before he harms someone else, this is about Aunt May, plain and simple.
I do want to mention a scene on page 17 where he slams the Martino's face into a wall, because his mask is off, but his face is obscured by shadows, and this is placed between two panels of him making threats with a plainly visible face. It seems as long as he's just talking, Peter Parker can stay in some form of control, but if Spider-Man starts to act, the anger gets ahold of him again, and the actions become the sorts of things we're unaccustomed to seeing from our 'friendly neighborhood Spider-Man'.
Amazing Spider-Man #541: There's one other thing I want to touch on in this issue. Page 4, last panel, as Peter swings away with the man who shot the man who shot Aunt May. In the the Aunt May scene, as mentioned previously, he was mostly illuminated, as he held on to May tightly - but carefully - around the torso as he brought her to the hospital. Now, he's shrouded in shadow, moving away from the hospital, and casually holding this man by the ankle. With May, peter was clearly worried too much movement might harm her; with this killer, I don't think Peter would mind if the man cracked his skull open on a roof Peter didn't clear by enough.
So, I've gone 'round and 'round this thing, and I still don't know that I figured out what the coloring was about. Part of me says it's the "emotional turmoil" answer, and my teachers always said that on multiple choice, if you weren't sure, go with your first instinct, because there's got to be a reason why you're picking that one. Still, I just don't feel like that's right, or that the coloring doesn't represent it properly if it does.
I think I've reached a wall, as far as ideas go, if you've got any, chime in, please. There's a lot more I'd like to look at just in this arc besides this, like the last few pages, when both Spidey and Kingpin are getting ready, and Peter's dressed in black, crawling through shadows, while Kingpin strides in the light, dressed in immaculate white. Or why so many police officers' faces were hidden in shadows in these issues (the guards at the end of #541, the cop outside the building Martino shot Aunt May from in #539, but not the cops catching the guy for public urination in #540. Odd).
But I think that may wait for another day, assuming I have any inspirations. Unless you've got some thoughts on those. We could just turn this into a big ole' art discussion.