Only two guesses in the past day so here are the leads. I can up with a new means of tallying so these should be accurate. See below the other clues:

337: Original TV character; 10s
338: From a TV show; based on comics; 10s
364: From a TV show; based on comics; 90s
380: From a TV show; original character I think but at least one Marvel character has same name; 10s
401: From a TV show; based on comics; 10s
414: This incarnation is an original movie character; 10s
415: Original TV character; 10s
431: TV character; more or less based on comics (it's a little complicated); 90s
432: From a TV show; based on comics; 90s
439. From a TV show; based on comics; 10s
441: From a TV show; based on comics; 10s
445: From a TV show; based on comics; 90s
458: From a TV show; based on comics; 10s
460: Original TV character; 10s
461: From a TV show; based on comics; 00s
467: From a TV show; counterpart with different code name of character based on comics; 10s
469: From a TV show; based on comics; 10s
470: From a TV show; based on comics; 10s
480: From a movie; based on comics; 00s
481: From a TV show; based on comics; 00s
486: From a TV show; group somewhat based on a single TV show character; 00s
489: From a TV show; based on comics; 90s
552: From a TV show; based on comics; 10s
569: Original TV character but related to character based on comics; 10s
599: From a TV show; based on comics; 90s
604: From a TV show; based on comics; 00s
612: From a TV show; based on comics; 70s or 80s
618: From a TV show; based on comics; 10s
621: From a TV show; based on comics; 00s
634: From a TV show; based on comics; 10s

Feature characters. Hulk and the Agents of SMASH=Hulk, Wolverine and the X-Men=X-Men, Avengers (future) can be either Next Avengers or Future Avengers; if a character appeared in multiple shows, I went with their first appearance:
Spider-Man: 8
X-Men: 7
Avengers: 6
Hulk: 3
Avengers (future): 2
Fantastic Four: 2
Blade: 1
Iron Man: 1

612. Spider-Man, Marvel Productions

Only two answers in nearly a day. I got ambitious and came up with clues for all 28 remaining characters, but if enough characters are identified today, I'll hold off identifying the specific continuities until Wednesday. And of course if everyone found as a result that will start the new round sooner.

337: Original TV character; 10s; there's something Inhuman about them
338: From a TV show; based on comics; 10s; there's something Inhuman about them too
364: From a TV show; based on comics; 90s; just a cameo on show; in the comics both a main and divergent version are prominent characters
380: From a TV show; original character I think but at least one Marvel character has same name; 10s; are you having trouble seeing them?
401: From a TV show; based on comics; 10s; prominent father character
414: This incarnation is an original movie character; 10s; doesn't want to be in a labyrinth
415: Original TV character; 10s; another hero you don't want to be invited to a drink with
431: TV character; more or less based on comics (it's a little complicated); 90s; usually closer in nature to Nicholas Hammond than Peter Parker
432: From a TV show; based on comics; 90s; part of some sort of future clan
439. From a TV show; based on comics; 10s; female version of a prominent villain (and a villain herself in comics)
441: From a TV show; based on comics; 10s; active in the future, though comics version was active in the present
445: From a TV show; based on comics; 90s; name refers to a type of normal body activity; this version also from the future
458: From a TV show; based on comics; 10s; comics version not a superhero; relative of other heroes using same code nmae
460: Original TV character; 10s; is high ranking royalty
461: From a TV show; based on comics; 00s; sibling to a more prominent hero in both show and comics
467: From a TV show; counterpart with different code name of character based on comics; 10s
469: From a TV show; based on comics; 10s; assuming show follows comic, leads the team they're on
470: From a TV show; based on comics; 10s; mutant in a show that isn't about mutants
480: From a movie; based on comics; 00s; movie set in the future but they were active in the modern era
481: From a TV show; based on comics; 00s; active in the future but comics version active in the present
486: From a TV show; group somewhat based on a single TV show character; 00s; active in the future but comics and earlier show versions active in the present
489: From a TV show; based on comics; 90s; also part of some sort of future clan
569: Original TV character but related to character based on comics; 10s; from future and likely relative of TV version(s) of comics character(s)
599: From a TV show; based on comics; 90s; once again part of some sort of future clan (same clan as 432 and 489)
604: From a TV show; based on comics; 00s; auditioned to join a team on the show
618: From a TV show; based on comics; 10s; father of a more prominent hero with same code name
621: From a TV show; based on comics; 00s; misguided antagonist hero due to father's actions
634: From a TV show; based on comics; 10s; uses a code name that their comics counterpart has largely discarded

Spider-Man: 7
X-Men: 7
Avengers: 6
Hulk: 3
Fantastic Four: 2
Avengers (future): 1
Blade: 1
Iron Man: 1

338. Iso, Ultimate

401. T'Chaka, Ultimate

431. Spider-Man actor, Spider-Man:TAS

599. Dawnsilk, X-Men:TAS

I'll update the list later but everyone correct. Sorry about the Flint error.

Not quite a day yet but want to give people a chance to reply before I head out: I've expanded/corrected the existing clues. Tomorrow around this time will reveal the continuities so by Thursday at the latest round 3 will begin.
364: From a TV show; based on comics; 90s; just a cameo on show; in the comics both a main and divergent version are prominent characters; 616 version has spent time in prison
401: From a TV show; based on comics; 10s; prominent father character seen in the second half of the last decade
415: Original TV character; 10s; another hero you don't want to be invited to a drink with; military
439. From a TV show; based on comics; 10s; female version of a prominent villain (and a villain herself in comics); she's armed in some fashion
441: From a TV show; based on comics; 10s; active in the future, though comics version was active in the present; legacy hero
445: From a TV show; based on comics; 90s; name refers to a type of G-rated sometimes involuntary body action; this version also from the future
458: From a TV show; based on comics; 10s; comics version not a superhero; relative of other heroes using same code name, so there's a bit of symmetry to them
460: Original TV character; 10s; is royalty of some sort and a Humphrey Bogart movie's title is a good descriptor; name sounds a bit like a last boy on Earth
461: From a TV show; based on comics; 00s; sibling to a more prominent hero in both show and comics; both serve on the same team sometimes in both show and comics
467: From a TV show; counterpart with different code name of character based on comics; 10s; this specific version from a reality that 415 would probably have a bloody good time in.
469: From a TV show; based on comics; 10s; assuming show follows comics and movise (and I have this feeling it might be the case), leads the team they're on
470: From a TV show; based on comics; 10s; mutant in a show that isn't about mutants; character's life is rarely just black and white but a bit of both
480: From a movie; based on comics; 00s; movie set in the future but they were active in the modern era; father of a main character in movie
481: From a TV show; based on comics; 00s; active in the future but comics version active in the present; there are c0omics teams in the plural in comics
486: From a TV show; group somewhat based on a single TV show character; 00s; active in the future but comics and earlier show versions active in the present; send in the clones
569: Original TV character; from future and likely relative of TV version(s) of comics character(s); sibling found late in part 1 of this collage series and appears to be named after ancestor
604: From a TV show; based on comics; 00s; auditioned to join a team on the show; comics version is a member of a different team; his powers are good for getting into locked locations
618: From a TV show; based on comics; 10s; grandfather of a more prominent hero with same code name; European but grandson is American
621: From a TV show; based on comics; 00s; misguided antagonist hero due to father's actions; comics version has been hero, villain, and supporting cast
634: From a TV show; based on comics; 10s; uses a code name that their comics counterpart has largely discarded; comics version's best friend also a superhero

Spider-Man: 5
Avengers: 4
X-Men: 4
Fantastic Four: 2
Hulk: 2
Avengers (future): 1
Blade: 1
Iron Man: 1

439. Lady Octopus, Radomski

467. Blood Spider, Ultimate—TRN577

480. Giant-Man, Next Avengers

481. Hellion, Yost—80920

401. T'Chaka, Radomski

486 is close enough (X-23 clones). The rest are correct. List updated.
364: From a TV show; based on comics; 90s; just a cameo on show; in the comics both a main and divergent version are prominent characters; 616 version has spent time in prison
441: From a TV show; based on comics; 10s; active in the future, though comics version was active in the present; legacy hero
445: From a TV show; based on comics; 90s; name refers to a type of G-rated sometimes involuntary body action; this version also from the future
458: From a TV show; based on comics; 10s; comics version not a superhero; relative of other heroes using same code name, so there's a bit of symmetry to them
461: From a TV show; based on comics; 00s; sibling to a more prominent hero in both show and comics; both serve on the same team sometimes in both show and comics
469: From a TV show; based on comics; 10s; assuming show follows comics and movise (and I have this feeling it might be the case), leads the team they're on
569: Original TV character; from future and likely relative of TV version(s) of comics character(s); sibling found late in part 1 of this collage series and appears to be named after ancestor
604: From a TV show; based on comics; 00s; auditioned to join a team on the show; comics version is a member of a different team; his powers are good for getting into locked locations
621: From a TV show; based on comics; 00s; misguided antagonist hero due to father's actions; comics version has been hero, villain, and supporting cast
634: From a TV show; based on comics; 10s; uses a code name that their comics counterpart has largely discarded; comics version's best friend also a superhero


Spider-Man: 3
Avengers: 2
Fantastic Four: 2
X-Men: 2
Hulk: 1