Expy/Web Original

Web Animation

 * Broken Saints has two villainous blondlieutenants named Charles and Bravado. Between the names and the haircuts, there is something very, very familiar about them...
 * Lord Zet and Nekoneko of the flash series Super Freakin Parody Rangers are deliberately obvious Expies of Zetto and Ruri from the creator's earlier work TTA.

Web Original

 * Suzumiya Haruhi no Yaku-Asobi is full of these. One particularly sprawling multi-RPer slider faction known as the Multiverse Enforcement Bureau employs what is practically an alternate SOS-dan, consisting of a long-haired half-American Trigger Happy Haruhi who's a stickler for keeping things orderly, Kyonko, the person Kimidori Emiri was 'based on' by the aliens (a Dojikko), the Student Council President from Seitenkan, a Cold Sniper Mikuru, and a Men in Black-ish Sasaki. No, really.
 * Dr. James Zanasiu, main character of the Darwin's Soldiers RPs is an expy of James Miardian, the scientist from the first RP that James's creator ever played: The Spreading Hazard.
 * Dr. Bailey, who first appeared in the rebooted Furtopia RP, was an expy of Dr. Shelton from the Gang of Five RPs, after the latter showed how useful it was to have a non-action tech guy around.
 * A fair amount of characters from Survival of the Fittest. Occasionally, you will see one of a character from a previous version or the original canon (for example, Melina Frost was clearly at least to some extent inspired by Mariavel Varella of v2, and possibly by extension, Mitsuko from Battle Royale). Other times, you will see ones of characters from other works, based on people the handler knows, or are imported from other roleplays the handler has participated in.
 * The Deviant ART group Earth-G is made of these who are DC superhero expies
 * Doctor Linksano from Atop the Fourth Wall is one for Doctor Insano from The Spoony Experiment. Justified in that Linkara created Linksano, because he felt bad about asking Spoony to play Insano for him over and over. And of course it's also lampshaded because he is Insano's counterpart from alternate reality.
 * Astholm on NationStates appears to be an expy of Scotland; or at least, Nottinghamshire, but it's all Depending on the Writer, what with it being a House Pseudonym and all.
 * In The Gungan Council, several characters use avatars from the Star Wars films, including C'oringath and Ceel. Others use avatars from the Expanded Universe. Usually, these characters even match their avatar's in personality.
 * Given the premise of the show, Coyle Command takes a lot of its characters from G.I. Joe. There is Coyle Commander (Cobra Commander), Anni (Destro), Countess Crossland (The Baroness), and COMMANDO (G.I. Joe itself)
 * The SCP Foundation has SCP-582, an expy of Slender Man. To be specific, both are Web Original Shared Universe horror stories with a mysterious recurring villain whose mere presence seems to cause death and madness, and both of which have elements of Clap Your Hands If You Believe.
 * She's still a three-dimensional character and takes inspirations from others too, but The Nostalgia Chick is fundamentally an older, more broken Daria.
 * The Saga of Pretzel Bob features as its villain a silver-haired man in a black cloak who sets the main character's hometown ablaze and wants to destroy the world... named Seraphoth.
 * The Whateley Universe is full of these, particularly since it's a superhero universe with a Super-Hero School.
 * Champion is clearly an expy of Superman, down to the freezing breath and the heat vision.
 * For that matter, Fantastico is an expy of Superboy, complete with the super-strength and the heat vision. Oh, and he might also be a pastiche of George W. Bush.
 * Dr. Yablonski is even lampshaded as basically being Batman as a physics teacher.
 * Aquerna has squirrel powers, including being able to talk to squirrels and command them. Who could that be?
 * Tennyo is Ryoko. Period.
 * Lady Hydra is The Baroness, although in-universe it is the other way around.