Misa Amane in Death Note was a Perky Goth, though her looks became more mainstream after the Time Skip to indicate her maturity and fame. In the anime, Misa wears outfits like this twice: once as she sings about her devotion to Light in the streets, and later in the Grand Finale... as she quietly stands atop of a rooftop, after Light's death — and it's strongly implied that she threw herself off it. As a matter of fact, it's possible that her original montage actually takes place directly before her scene in the finale, which may be why she, in the montage, is seen on a rooftop looking forlornly at the horizon. The outfit may have been so distinct specifically to draw us to this conclusion.
The manga Doll by Mitsukazu Mihara is filled with tons of characters wearing lolita, specifically the Dolls (androids) of the story. Mihara also did the first covers of the Gothic Lolita Bible.
In the second season of Genshiken, the males discuss what Ogiue would be like as an ero-game character. The answer: she would be a shy girl in a Gothic Lolita dress who would nevertheless be sexually aggressive even if it was her first time.
Kanako from Love Hina Again; she even persuades Keitaro to dress in a goth-like manner briefly. Check out the credits for that episode of the miniseries, which have the other characters, save Haruka, similarly... modified. The cover of volume 11, in which Kanako first appears, has all the characters except Keitaro dressed in this style. Keitaro's not on the cover because he happens to be away until the last three pages of the book.
Cosette d'Auvergne from Le Portrait de Petite Cosette.
Before changing families Senko Himemiya's (later known as Chika Midarezaki) standard outfit was of this variety.
There is also the random shots at the end of the opening video where the female family members are seen wearing EGL.
Everyone and everything from Black Butler. (With, of course, the guys tending more toward Elegant Gothic Aristocrat.) Even grim and steely little Ciel Phantomhive wears tiers of lace and roses spilling off his top hats.
In Loveless, Nagisa's outfits are all traditional gothic lolita. Yes, even when she's at home or eating lunch.
Evangeline A.K. MacDowell (on the picture above together with Chachamaru), who dresses like this all the time when not wearing her school uniform. In one chapter of the manga, Evangeline takes on Asuna as an apprentice and demands that she dress only in gothic lolita style. In another, she dresses those still at school campus during the holidays in cosplay/Goth Loli, because she's bored. The fanboys were entertained, at least.
Isabella dresses in Elegant Gothic Aristocrat style, which is basically Elegant Gothic Lolita with floor-length skirts and a more ladylike look. Probably because it's hard to pull off the lolita part when you're a six-foot-tall transsexual.
Miwako Sakurada sometimes dresses in Sweet Lolita dresses.
Venus Versus Virus has Lucia, and she also has a clothes' store that sells dresses in the same style. The twins Layla and Lola also dress in gothic lolita fashion, and many of Sumire's outfits have gothic lolita overtones.
In The Wallflower (Or Yamato Nadeshiko Shichi Henge), there's the "GothLoli Sisters" who are rather less than elegant, not very lolita-ish, and also not very gothic... but that's what they call themselves, and often chant "Goth Goth Loli Loli".
Anna Kushina in K is 11 years old, has very doll-like skin and white hair and wears a frilly red dress and matching ribbons on her hair. She really stands out since the rest of the members of HOMRAnote the organisation she participates in are dressed like gangsters or thugs.
In one episode of Yu-Gi-Oh! GX, Judai had an opponent named Alice who dressed like this.
Cathy dresses this way in Yu-Gi-Oh! ZEXAL (but only when she duels; other times, she wears a more modest schoolgirl outfit).
In Detective Conan, a whole case features a lolita fangirl, Mihiro Kuze, as the murder victim. At the very start we get to see her wardrobe and she's in possession of quite a bit of EGL clothes and jewelry, which borders as a case of Costume Porn in the animated version. Later she's found dead in a public restroom and since Conan, Kogoro, Ran and Sonoko were among those who saw her alive last, they now have to testify and investigate her death. The fact that she's a lolita is vital in the resolution, as her black dress is one of the proofs against her killer: her former best friend Yuika, who had actually worn it before the murder to create an alibi... and she also had it on while she was killing Mihiro.
The trope also gets lampshaded when the victim is seen in the tea parlor for the first time. Or so we think. Kogoro is weirded out and speaks about "that eerie witch costume" she's wearing, but Ran and Sonoko go all "GOTH LOLI, SO CUUUUUUTE ~ !"Of all people, Conan explains to him what Goth-Loli is, and then he thinks that Ai would fit in the subculture fairly well (complete with a Imagine Spot of Ai in a gothloli dress). Later Megure is weirded out at the sight of Mihiro's lavishly-dressed corpse and snarks at Takagi when he explains what Gothloli is.
Nonon Jakuzure and Nui Harime of Kill la Kill wear a Casual and Sweet Lolita style respectively.
Madoka Kaname from Puella Magi Madoka Magica. She dresses rather normally most of the time, but her Magical Girl outfit looks like it's straight-up taken from the wardrobe of a Swet Lolita fan — has a puffy skirt, lots of frills, huge ribbons and super cute shoes with frilly knee-length socks. The Gothic aesthetic fits as well, as Puellae inevitably mutate into Germanic or Victorian-themed Eldritch Abomination Witches.
Mami Tomoe's outfit, save for the Magic Skirt, would fit in pretty well in Casual Lolita.
Many of the outfits in Il Sole penetra le Illusioni. Etia and Ariel are full-on gothic lolita, and Akari and Luna have some gothic lolita inspiration in their normal clothes.
Marvel's Livewires miniseries featured a character actually ONLY named Gothic Lolita, who served as the Cute Bruiser of the title Five-Man Band. To be fair, she is a self-named Robot Girl, and her teammates have equally odd monikers.
Also from Marvel, Runaways leader, Nico Minoru, is referenced as such in the comics first script.
Kim Pine during the gig in Scott Pilgrim and the Infinite Sadness.
Ever After High features this heavily, for obvious reasons. Can't sell plain looking characters as dolls, now, can you? But... It does not match the guidelines for the style at all, though, so it's kind of subverted, although the general silhouette and certain accessories and decorations of some characters look very lolitesque, the clothing of the girls looks like a fairy tale/fantasy re interpretation of Lolita.
Little Miss Badass Latooni Subota finds herself turning into this. First by accident, second in order to match her with the Princess she was assigned to guard, and finally ordered into it by one of her superior officers because frankly, she looks so damn cute in it. To be fair, however, every time she wore that dress, she ended up with a fair amount of Character Development, and the officer giving the order actually says as much.
And don't get us started on her giant robot. There's a reason the game's development staff nicknamed it the Gothlolion.
Yurika Kirishima of the Rival Schools sequel Project Justice dresses in this style (and her profile even lists a like of frilly and lacy clothing) but the colors of her clothing (light blue dress and a bright red ribbon) contrast to the typical dark colors associated with this trope.
In the Tales of Ash saga, a girl from Those Of The Past dresses like this. She's a very creepy-looking Emotionless Girl named Rimelo, never seen without her partner Shroom. In XI they attack the Ikari Warriors to steal Magaki's body, stealing Heidern'sEyepatch of Power in the meantime; in XIII they ambush Kyo Kusanagi to give him his KOF invitation, in the Story mode she stands by Shroom's side as he speaks to Ash Crimson, and she's also there when Shion returns to this world in the ending.
The "Dark Beauty" dress Cordelia can acquire in Shadow Hearts: Covenant is, appropriately enough, in this style. In From The New World, Hilda is the fashionista.
In The World Ends with You, Lapin Angelique, the store in A-East, carries Gothic And Lolita attire as its main stock.
Mountain Of Faith's second boss, Hina Kagiyama, Undefined Fantastic Object's sixth boss, Byakuren Hijiri, and Phantasmagoria of Flower View's Medicine Melancholy are actually some of the few who fully represent this trope.
Also, series protagonist Reimu herself started as a rather traditional Miko whose outfit was progressively wa-lolified.
Rock Band has a handful of frilly, lacy articles of clothing, thus allowing you to dress a female custom character like this if you want. There are also a few items suitable for an Elegant Gothic Aristocrat.
In Immortal Souls, all of the women in one of the vampire gangs dress in a style like this. Which leads to the rather quirky visual of the buff, trenchcoat-clad main character getting his ass kicked by girls wearing corsets, frilly skirts, and Parasols of Prettiness.
Every female character in Death Smiles dresses like this, most likely because they're in a world reminiscent of early 20th century Europe - in the endings, any girl who returns to the real world is generally seen wearing more mundane clothes.
In Style Savvy: Trendsetters, the brand "Raven Candle" exclusively specializes this type of clothing. The "Marble Lily" brand mostly specializes in frilly princess fashions, but their darker-coloured clothing occasionally strays into this territory as well. There are a lot of customers who have or want outfits in this style, and you can dress your character in them as well.
In Little Busters!, Komari's casual outfit is a cute gothic lolita outfit. Which is probably great evidence of the sheer extent to which gothic lolita has overtaken every other kind of lolita in Japanese media, because while Riki notes correctly that the innocent doll-like aspects of the fashion suit Komari perfectly, the gothic part very much doesn't, while in contrast the sweet lolita subgenre, with its colorful sweets, stars, and fairytale themes, would fit both Komari's general personality and the themes of her route almost impossibly perfectly.
Daryl: Breanne Geothe? The midget in the gothic outfit who likes some witch stuff?
Chimera, from the 3rd season of Winx Club, is a GothLoli. It has been criticized that Stella should know this (especially since it's a well-known fashion style), but she doesn't act that way, calling her look "pre-teen meets goth".