Alpha Centauri
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Method Man has LOADS, too many to name.
One of them, from memory, on the song Triumph by Wu-Tang Clan:
"Out of the frying pan, into the fire/Transform into the Ghost Rider.". His nickname is Johnny Blaze, on top of that.
Another Method Man one from The ?:
"Control hammer like the mighty Thor/Bringin' thunder down.".
Ghostface Killer has two Marvel-based nicknames: Tony Starks and Ironman (Was a cameo for him in the movie, it's a deleted scene).
From Protect Ya Neck by Wu-Tang Clan (Inspectah Deck):
"Swingin' through your town like your neighborhood Spider-Man.".
M.F. Doom features Dr. Doom on a lot of his art, wears a metal mask.
One from Vast Aire (Also Blueprint), on the song Zenith:
"I understand all the reasons for pain/That makes my soul metal like Logan's skeletal/Adamantium in the core within.".
From the same song (Blueprint):
"Burn your face like the depths of Hell/I'm like a wolverine with an adamantium shell.".
From Stress Rap by Cannibal Ox (Vast Aire):
"They used to call me Crazy Joe, add a bazooka/Now they can call me Batman; beyond your manuevers.".
From Battle for Asgard by Cannibal Ox (Vordul Mega):
"We mind-bogglin', spine-tinglin'/Got the scroll of Galactus now I'm planet-swallowin'/Megala's got the surfboard and he's hollerin'.".
The obvious references to Asgard and also one to Odin COULD be considered a Marvel ref, given the aformentioned ones, but I don't want to assume.
Some from Nrrd Girl by MC Chris:
"She's more like a wallflower/Like the one that Stryker sniped/I'm like elixir when I'm with her cos I think I like her type.".
"Always ravin' 'bout her favs/Wanna conquer her like Kang, when you kiss like Cassie Lang.".
"X-23 and Hellion, odd couple, to be kind/She's in my heart, in my mind and now she's in my rhymes.".
From My Name Is... by Eminem:
"Clothes rip like The Incredible Hulk/I spit when I talk/I f*ck anything that walks.".
Also, I think I recall one from Purple Pills by D12, during Proof's verse:
"I thought I was incredible and killed the Hulk.".
Paul McCartney did a song called Magneto and Titanium Man I believe.
Additionally, I believe the M.C. David Banner bases his name off the T.V. show.
I know of a rather excellent female M.C. named Jean Grae.
Not all lyrics, but references.
-AC