Clark Kent/Superman. For that matter, Superman's entourage of people with the initials "LL"; Lois Lane, Lex Luthor, Lucy Lane, Lana Lang, Lara Lor-Van, Lori Lemaris, Linda "Supergirl" Lee, Lyla Lerrol, Letitia Lerner, etc. The first two were coincidence; after that, the writers picked up the theme and ran with it. Also note that Kal-El read backwards also has two L's.
There was a Superman story back in the Silver Age that involved a threat against "someone close to Superman". There was a clue left in the form of two steel girders formed into a giant LL. Superman's reaction was along the lines of "Oh, great, that's real helpful."
The Post-Crisis Superman continuity included a sort-of Superman lookalike named Bibbo Bibbowski, who was a longshoreman and former boxer.
Smallville continues the double-L theme: Lana Lang's parents are Lewis and Laura Lang, and Lex's dad is Lionel Luthor. Lionel's parents? Lachlan and Eliza. (Several of these were already obscure comics canon.)
Lex's mother name was Lillian and in a dream universe his daughter with Lana Lang was named Lily, and his hallucination on a desert island that was obviously himself was called Louis Leery.
Subverted by Lex's actual given name: Alexander Joseph Luthor.
Marvel's Age of the Sentry showed the Sentry's Silver Age adventures in more detail, and revealed that like Superman he seemed to encounter a lot of people with the same initials, but in his case they were "EE". The Sentry's real name is Robert Reynolds, part of the subversion they were going for with the character when they said that he was actually invented by Stan Lee and then forgotten about among a stack of old story notes. He goes by Bob though.
Similarly, Batman once had a series of alliterative romantic interests, including Vicki Vale (played by Kim Basinger in Batman) and Silver St. Cloud.
Calvin "Cave" Carson, a Silver Age spelunker-adventurer.
Max Mercury, a time-traveling speedster with ties to The Flash, who also used the name "Whip Whirlwind" in the 1890s.
Sargent "Sarge" Steel, one of the Charlton Comics heroes purchased by DC. ("Sargent" is his name, not a rank.) Originally a hard-boiled detective/spy-smasher type, he became a government official in charge of many of the DCU's superhero-related agencies.
Tex Thompson, aka "Mr. America" and "Americommando", a spy-smashing superhero introduced in Action #1 along with Superman. He's been revised and retconned several times since then.
The original characters in the Marvel Universe co-created by Stan Lee were often given alliterate names as a mnemonic device.
Peter Parker/Spider-Man. Among others, he had to deal with J. Jonah Jameson and Otto "Dr. Octopus" Octavius. Jonah himself has a son named John Jameson by his first wife, Joan, he later married Marla Madison, his editor-in-chief is Joe "Robbie" Robertson (who has a son named Randy), and secretaries have included Betty Brant (whose brother was called Bennett) and Glory Grant. The Bugle staff absolutely adores alliteration. In fact, it was recently revealed that JJJ is actually J. Jonah Jameson, Junior. We have also Curt Connors, the Lizard, and Cletus Kasady, a.k.a. Carnage. This reached the height of absurdity with a splash page showing the characters attending a Bugle funeral. Of the ten characters named, nine had alliterative names, with only Aunt May not fitting in.
Based off this, there was a Funny Animal version, named Peter Porker, The Amazing Spider-Ham, who worked for J. Jonah Jackal.
The novelization of Spider-Manhung a lampshade on this, by having Jameson name the Green Goblin in a headline. This resulted in a brief discussion on alliteration between J. Jonah Jameson, Peter Parker, the Bugle's editor Robbie Robertson, and Jameson's secretary Betty Brant... none of whom seemed to notice they were examples. The same point is made out in Spider-Man 3.
As if to make his Expy-ness of Spider-Man more obvious, Hazmat of the Imperfects has the alter ego of Keith Kilham.
Scott Summers/Cyclops and Warren Worthington III/Angel of the X-Men.
Fantastic Four members Susan Storm/The Invisible Woman (although she changed her name when she married) and Reed Richards/Mr. Fantastic
Stephen Strange/Doctor Strange, Master of the Mystic Arts (and sometime Sorcerer Supreme)
The various principalities and powers, and the effects they conjure, tend to be alliterative as well (e.g. the Blinding Brazier of Balthakk, the Hoary Hosts of Hoggoth). Justified, since magic involves chants and spoken spells, and alliteration is a memory aid.
Pepper Potts, Tony Stark's assistant and/or love interest from Iron Man. (Although her first name is actually Virginia, she is best known by her nickname.) Doubles as a Punny Name. She is the team coordinator for The Order, which had a distinct majority of this among its ranks. Henry Hellrung, Rebecca Ryan, Magdalena Marie (born Magdalena Marie Neuntauben, though), Avery Allen, Pamela Pierce, and Carlos Carvaho were all members of the team at some point or another — just under two thirds of its all-time roster.
Millie the Model, as well as other "career girl" features that Marvel Comics debuted around the same time: Nellie the Nurse, Sherry the Showgirl and Tessie the Typist.
Bruce Banner/Incredible Hulk. (The alliteration didn't save Stan from calling him "Bob Banner" in an early story, thus enshrining in canon the full name of "Robert Bruce Banner".)
In the TV series, it was changed to David Banner (with Bruce as a middle name) because of directorial distaste for this trope. At least that's what Kenneth Johnson (the producer and writer of the bulk of the series) says. Stan Lee says that the producers thought the name "Bruce" sounded gay. See, back in the funky '70s the name Bruce was thought of as a "gay" name the United States.
Slight variation in the British comic strip George And Lynne (featured in The Sun) — the title characters seem to know a lot of couples who have first names beginning with the same letter (such as Dave and Donna, or Jack and Jenny).
Lots of examples in Archie Comics: Archie Andrews, Jughead Jones, Coach Clayton, Dilton Doiley, Moose Mason (full name plus nickname Marmaduke Merton Matowski "Moose" Mason), Waldo Weatherbee, Trula Twyst, Evelyn Evernever, and a few others. Some are nicknames or titles, but it still fits.
Stephen Stills of Scott Pilgrim, as well as four of Ramona's "Evil Exes": Gideon Graves, Roxy Richter and the Katayanagi twins (Kyle and Ken).
Many characters in German comic strip Nick Knatterton. (Barbara Beerbottle, Felix Finster...)
In stories by Wilhelm Busch: Max Und Moritz, Hans Huckebein, Kuno Klecksel, Balduin Bählamm, and others.