From memory, there’s also Captain Triumph.
I just got a book called The League of Regrettable Superheroes: Half-Baked Heroes from Comic Book History, by Jon Morris. In addition to a couple of the ones from Cartoonacy’s list, it includes Captain Truth and Captain Science.
I saw this thread and immediately thought of General Disarray (South Park).
It had to annoy Captain Atom that he was outranked by his nemesis, Major Force.
A couple decades ago I created my own superhero, Captain Apple. He was intended to be a spoof on the local apple industry.
Are you based in Cupertino? 
Captain Lance Murdock of The Simpsons must qualify as a superhero. After all, he’s survived unbelievably horrific accidents and comes back for more. (And with a last name like that, he is no doubt related to Daredevil.)
Nope, 
This.
Captain Deadpool. No just…just Deadpool. That sounds like a fucking franchise!
I’ve often wondered what Captain America would call himself if Steve Rogers got promoted to Major.
Or maybe Macgyver’s nemesis, who likewise cheats death many times.
Being the Captain of a ship, or Navy/CG installation, is just as real as having a rank of Captain.
And his sidekick Private Parts
Major 'Merica, of course.
I think it’s a combination of those two. A rank high enough for command but low enough to have horrible people telling him what to do, that makes for good storytelling, and all the other words other than Commander are also adjectives. Commander just doesn’t have the zing that Captain does, plus would probably be older than a Captain.
There’s a DC hero called Commander Steel.
I call dibs on “Colonel of Truth.”