Spoofed in "Homer to the Max" when Homer changes his name to Max Power ("I got it from a hair dryer"). Homer also suggested Handsome B. Wonderful, Hercules Rockefeller, and Rembrandt Q. Einstein; the judge allowed Max Power because it was the only one he had spelled correctly. He also suggested new names for Marge including Chesty LaRue, Busty Sinclair, and Hootie McBoob.
While on the lam in "The Dad Who Knew Too Little", Homer and Lisa check into a hotel. Lisa calls herself "Lady Penelope Ariel Ponyweather". Homer tells the clerk that his name is Rock Strongo. The clerk immediately calls Homer out for using such an obvious fake name and asks for his real one.
Homer: ... Lance Uppercut. Clerk: Sign here, Mr. Uppercut.
Homer has also used the alias "Elvis Jagger Abdul-Jabbar."
Bart says he's going change his name to Joe Kickass. Homer suggests Homer Junior. "The kids could call you HoJu!"
Homer's one-time boss Hank Scorpio.
Rainier Wolfcastle Pronounced "Rain-ier" Wolfcastle. Just say that name, it's awesome as hell.
In American Dad!, "Irregarding Steve" has a Fake Action Prologue where Klaus turns out to be a world-saving action hero, and he tells Francine his real name is "Professor Max Hammer."
Teenage Mutant Ninja Turtles: Donatello, Leonardo, Michaelangelo, Raphael, Master Splinter. Moreso in 2K3 where they occasionally use the surname Hamato. There's also Shredder, Krang, Bebop, and Rocksteady.
Wild West C.O.W.-Boys of Moo Mesa had a ton of great names like Moo Montana, Cowlarado Kid, Dakota Dude, Buffalo Bull, Lilli Bovine, Cowlamity Kate and many more. The villains had some great names also, like the Masked Bull, Bat Blastagun, Skull Duggery, Shock Holiday, Boothill Buzzard, Saddlesore Scorpion, and plenty of others.
The Replacements: Dick Daring, Ace Palmero, Travis Bodie, and in what might be the straightest possible example of this trope, Sierra McCool.
After being mutated into animal hybrid things by a mad scientist, a few characters in decide to ditch perfectly ordinary names like Derek in favour of identifying as Claw, Fang and Talon. They don't need to hide their previous identities; they do it just because.
Originally, the Gargoyles didn't take names of their own, although their leader was known as Goliath by the humans they protected. When they found themselves in 20th century New York they took on names fitting to their new surroundings; Hudson (the old veteran), Brooklyn (the tough guy), Lexington (the smart skinny guy), Bronx (the dog), and Broadway (the mellow one).
The Rocket family (father Ray, daughter Reggie, son Otto) from Rocket Power. It's heavily implied (or at least NOT implied otherwise) that "Rocket" is their actual last name. The viewer is never given a reason to think that it's not, and that's good enough.
Some Transformers just luck out with the names. Slugslinger, Caliburst, Optimus Prime, Megatron, Starscream, Ironhide, Devastator, Bonecrusher, Wreck-Gar, Ultra Magnus, Thundercracker, Demolishor, Sunstorm, Dirge, Ruination, Sinnertwin, Gutcruncher, Scourge, Rampage, Mixmaster, Soundwave, Starscream, Razorclaw, Omega Supreme, Sentinel Prime, Elita One, Moonracer, Silverbolt, Superion, Fortress Maximus, Big Daddy, Grimlock, Ravage, Slayride.
Optimus Prime's name before he became carrier of the Matrix of Leadership (and thus a Prime)? Orion Pax. Megatron also named himself after "Megatronus", who is the TF equivalent of Judas Iscariot and Cain rolled into one (and thus became known as The Fallen). Also see the other members of The Thirteen.
Optimus Prime's combination with Omega Supreme has the name Optimus Supreme, which is a fairly normal name, until you realize "Optimus" in latin means "Best" Supreme means, well, best, so his name literally trasnaltes to "Best best". Sadly, Omega Prime would have been even more bombastic a name, since Prime refers to the "First", essentially turning the name to "The alpha and the omega".
The Headmaster of School For Vampires has a name that could only be given to a truly badass vampire: Count Alarich von Horrificus.
Billy's name for an alien dog-thing: "Admiral Wolverine Lightningbolt, because those are the three coolest words in the universe!"
There's also DelGado. Hoss DelGado.
While the girls of Sky Dancers got off pretty easy, the guys ended up with the names "Slam" and "Breeze".
In G.I. Joe, every single member of the G.I. Joe organization had a nickname. Most had nicknames relating to their specialties: Doc was a doctor, Lifeline was a medic, Torpedo was a submarine pilot, Mutt had an attack dog, Alpine was a mountaineer, Snow Job specialized in fighting in the snow, etc. Some of the names were meaningful for other reasons, as in the case of redhead Scarlett. Some of the names, though, were just cool, like Duke and Lady Jaye.
Darkwing Duck was full of these, along with the title character. Especially with the villains like Megavolt, The Liquidator, Steelbeak, Splatter Phoenix, and many more.
Lord Monochromicorn and Princess Bonnibelle Bubblegum from Adventure Time.
Also Goliad, the name of Princess Bubblegum's immortal creation. It kinda sounds like the title of an epic. Go on, say it: GOLIAD!
Lady Rainicorn, Marceline Abadeer (aka Marceline, the Vampire Queen) and her gender-swapped alter ego Marshall Lee, Hunson Abadeer, Simon Petrikov, Susan Strong, Earl of Lemongrab, Ancient Sleeping Magi of Life-Giving, NEPTR (an acronym for Never Ending Pie Throwing Robot), BMO (pronounced BEE-mo), Tree Trunks (a pygmy elephant), and even the main character Finn the Human. In fact there are more awesome names than not in Adventure Time.
And while we're talking about it, the multitude of Princesses are also pretty rad: the aforementioned Princess Bonnibelle Bubblegum, Lumpy Space Princess (aka L.S.P.), Irregular Topography Expanse Princess, Truth Field Projection Princess, Princess Chewypaste, Princess Monster Wife, and Princess Princess Princess.
In My Little Pony: Friendship Is Magic we have Rainbow Dash, who has one of the coolest names a fictional horse can have. This is even more epic and meaningful when you see her pull off the legendary Sonic Rainboom.
Like him or not, Flash Sentry is a pretty cool name.
In this skit on Robot Chicken, Calvin joins G.I. Joe, and says that since he's a Cold Sniper, he'd like his codename to be: "Dead-Eye", "Killshot", "Dr. Killshot", "Sureshot", or "Triggerman". Unfortunately, he slips, so they call him "Fumbles". They pay for it. Dearly.
Was the plot of an episode of Regular Show. Rigby, after seeing one of his favorite bands on television, hears the superstar rocker The Edge (which is his literal name) tell about the origins of his name. Rigby then decides to choose two random sounding words, coming up with Trash Boat. Needless to say, once Mortecai finds out, Hilarity Ensues.
However, in an ironic (and very Regular Show-ish) manner, it turns out that Rigby's new name makes him extremely famous. However, this has a worse downside, as The Edge, now a superpowered wizard rocker, returns from the future to kill him because the name Trash Boat made Rigby more famous than The Edge, himself.
It helps that after the situation is cleared, The Edge suffers a Karmic Death at the hands of another superpowered wizard rocker, who in turn is killed by another. Who is killed by another. Who is killed by more. Can anyone say chain reaction?
Centurions gives us Max Ray, Jake Rockwell, Ace McCloud, Crystal Kane, Rex Charger, and John Thunder.
In Bolts And Blip, there's Tigrr Jaxxson, the most shiny, athletic, and proud player on the main characters' team.
The titular Steven Universe is a decent example. (His dad was named Greg Universe. From his mother, he inherits the middle name Quartz, making his full name Steven Quartz Universe. Rad.)
Grojband gives us Corey Jaron Riffin, which is supported in the episode "Dueling Buttons", when he inputs his initals in the game and they read "CJR".
Disney's Big Bad Wolf. His full name is Zeke Midas Wolf.