Interestingly enough, Spider-Man's origin story does not specifically mention any changes to his genitals. We do know that he grew much stronger overall (possibly relevant) and that he can stick to things (definitely relevant). It's not only his hands and feet that can stick to walls, it's his entire body (we've seen Spidey prevent his mask from being pulled off by making his face sticky). Essentially, this means he can lift large objects, like a briefcase or some lumber, with his super-strong penis. This has rarely come up in the comic.
As seen in the recent film The Wolverine, old James Howlett (aka Logan, aka Wolverine) can regenerate any part of his body, including his bones, and including his boners. Much like his claws, were his phallus to be chopped off, he would quickly grow a new one. Wolverine should consider himself lucky that the Weapon X project didn't simply use him as a factory for creating infinite transplant dicks to sell to victims of unfortunate accidents.
This mutant stands 9'5" and 1900 pounds. Either his penis is proportional to his body, and thus hilariously too large to be sexually practical, or it is an average human penis size, and thus hilariously too small for his giant body. In either case, it's hilarious, which explains why he's so pissed off all the time.
The Destroyer of Planets, Lord Galactus, is not actually a Caucasian man in armor who stands taller than the planet Earth. The way he appears is subjective to the observer, and most comics writers are White men. Skrulls would see him as a giant Skrull in armor. His junk is as large as you imagine it, and the answer will reveal things you never knew about yourself.
It's purple, right?
M.O.D.O.K.'s proportions lend themselves to a strange naked body under all that armor, so one might wonder what his M.O.D.I.K. looks like. But do not Google "MODOK without armor" or you will see a fan-made comic in which a naked M.O.D.O.K. smooches women in a hot tub. You will not un-see this image.
Where is his dick?
Compared to the Thing's probably-rocky Little Thing and the Human Torch's likely-to-ignite-upon-excitement...lower torch, Mr. Fantastic got the best deal when it comes to cosmic radiation penis mutation. In addition to being able to stretch his member to any size, Reed Richards can most likely contort it in a variety of shapes and directions, as he does with his weird neck and arms. Plus, he could easily have sex in the bedroom and work in the lab at the same time. Efficient!
You thought you were worried about shrinkage!
The superhero penis question begins and ends with the Hulk. The initial thought process goes like this:
"How come Bruce Banner's shorts turn purple when he transforms? Wait, why don't his pants tear off like the rest of his clothes? Oh, so you don't see his- WAIT, WHAT DOES IT LOOK LIKE?"
Common sense would dictate that the Hulk's dong is green; we can all agree on that. But if it's proportional, shouldn't there be a huge bulge in those shorts that are straining to keep from tearing? With that level of adrenaline, shouldn't he be erect upon transformation? How come the Hulk doesn't run around trying to fuck volcanoes?
"I wanted my Hulk to be naked..." said Ang Lee, director of the 2003 film Hulk, in an interview later that year, "...The Hulk's pants stay on because they want a PG-13 rating." Of course, actor Nick Nolte, who plays Banner's father in the film, had the (dubious) last word.
"I've seen a nude picture of him. It's not pretty. It could be used as a weapon, believe me."