Still if you read any comic book sites it's been impossible to avoid. People have been going crazy over one particular image that they think implies which heroes may have been replaced.
Either they're completely wrong or the author of the series (Brian Michael Bendis) isn't doing the basic groundwork on the character's histories.
Here's the shot which features a group of heroes (wearing 1970's and early 80's versions of their costumes) emerging from a crashed space ship:
I'm not completely familiar with every aspect of all of those characters but the majority of them have had events occur to them since this point which mean the hero we've been reading about can't be a Skrull.
Before I get into that I have a few notes on continuity. My feeling on comic book continuity is that the major events involving characters have to count but the tiny details can slip. By dropping in characters from the past like this Bendis has opened himself to continuity complaints. So while I'm ignoring the fact that the Skrulls all had their shape shifting abilities removed in the mid-80's and were stuck in their natural forms (everyone seems to ignore that brief storyline) I'm not ignoring the story lines for character's first appearance and other major transitions.
In addition I'm assuming that the Skrulls are not omnipotent and that supernatural beings are not going to bother covering up for their plans in order to screw with people.
So let's get started.
White Queen
Replaced by Skrull? Impossible.
Since she wore that costume the White Queen has swapped bodies with multiple people.
Spider-Man
Replaced by Skrull? Impossible.
Recently sold his soul... er... marriage to the devil.
Beast
Replaced by Skrull? Possible but unlikely.
I'm not aware of any specific events that exclude the possibility but the Beast has been directly involved with a lot of people who should be able to tell the difference.
Luke Cage
Replaced by Skrull? Could be.
Cage has some nice gaps in his life which could be used to justify a replacement and I'm not aware of anything that means he could not be a Skrull.
Thor
Replaced by Skrull? Not a chance.
Since that point he gained the power of Odin, triggered Ragnarök, been revived from the afterlife, and that's just the obvious ones. As a god Thor would be particularly difficult to replace successfully.
Wonder Man
Replaced by Skrull? Impossible, but if there's a character for them to get wrong I'd bet on him.
Wonder Man has died and gone to the afterlife since he wore that costume. Repeatedly. Since dying reveals if the person is a Skrull we know Wonder Man is not.
Invisible Woman
Replaced by Skrull? No way.
Went to heaven and met God recently. I think he'd mention something like that.
Phoenix/Jean Grey
Replaced by Skrull? You're kidding, right?
Phoenix is a cosmic entity and after she died it was revealed that she was a substitution for the real Jean Grey who returned. I can't even wrap my head around the problems caused by saying she was replaced by a Skrull.
Hawkeye
Replaced by Skrull? Seems the most likely.
There's a few minor events that would preclude the possibility but his continuity is so tangled now that it easily allows for a few replacements.
Iron Man
Replaced by Skrull? Could be but don't bet on it.
I'm not aware of anything in Iron Man's history that specifically prevents him from being a Skrull (the Crossing's multiple layers of retcons can still work with a Skrull) but since it's the obvious one then he won't be.
Vision
Replaced by Skrull? Impossible.
Got married and had children who in a pointless retcon of their own were a chunks of a demon. For him to be a Skrull requires that Mephisto is in on their plan and helping them with it.
Scarlet Witch
Replaced by Skrull? No way.
Responsible for reality shifts at the heart of two recent Marvel large scale crossovers. If the Skrulls can rewrite reality to their whim then why bother with the invasion plan?
Jewel
Replaced by Skrull? Interesting but unlikely.
One of Bendis's own creations, she's retconned into Marvel history. Since she's one of his favorite characters I think it's unlikely that Bendis would invalidate her entire history but it would work and be an interesting choice.
Mockingbird
Replaced by Skrull? Impossible.
Died, went to hell, and has interacted with many characters who were on day trips there over the years.
Captain America
Replaced by Skrull? Nope.
Besides the fact that he had a very public "death" which would have revealed a replacement there's the meta reason that he, like Iron Man, is a character people are supposed to think has been replaced so he won't be.
Ms. Marvel
Replaced by Skrull? Not possible.
After she changed costumes and joined the Avengers she had her personality and powers completely drained by Rogue. Rogue kept her powers indefinitely and had a split personality with her for some time and didn't gain Skrull shape shifting.
Wolverine
Replaced by Skrull? Well...
Not by "a Skrull" but by an elite team of seventy Skrulls which allow Wolverine to be an active member of four different superhero teams while pursuing his own adventures in three different books and guest appearing in half a dozen others each month.
So in conclusion, just about everyone on that ship will be a Skrull except for a couple token surprises, and most of the people who saw them come out of should realize this with just a few seconds.
