Suguha in Sword Art Online begins to fall in love with her brother Kazuto (who is actually her cousin) whom she knows is in love with another girl. In order to forget about those feelings for him, she tries to fall in love with an online person she met called Kirito. Kirito is Kazuto's online persona. When she figures this out, it breaks her heart since she's fallen in love with the same person twice.
Anzu/Téa in the Yu-Gi-Oh!manga and anime is frequently confused about whether she's in love with Yugi or "the other (Yami) Yugi." Obviously lampshaded in the abridged series.
Téa: Um... Yugi, before you go, there's something I need to tell you.
Yugi: Don't worry, Tea. I know all about it.
Yugi: Yeah. You're in love with me, right?
Téa: Actually, I'm in love with your sexy alter ego.
Yugi: Oh... this is kinda awkward.
Even worse, the fact that he's Yugi's alter-ego isn't even a secret for that long - she KNOWS that they're the same person, but she can't help but prefer the Other Yugi. Harsh, man.
Yuuki in Mugen Densetsu Takamagahara: Dream Saga is actually the main character, and all over both Takaomi and "that other guy named Takaomi with the same mark on his head but a totally different personality".
Tokyo Mew Mew complicates things. Ichigo loves Masaya, who loves Ichigo but also Mew Ichigo, and then in comes Ao no Kishi, and he loves Mew Ichigo, and she's stuck between not only this guy but also her Unwanted Harem. Then comes the traditional trial of every Magical Girl's Mysterious Protector, and we know that can't be good.
The manga / anime Cats Eye: The main characters are barmaids and part-time Spy Catsuit thieves. One of them has a boyfriend, who happens to be a police officer, and who cannot make up his mind if he likes his girlfriend or her Secret Identity more. (This, obviously, is the cause of much frustration on the main character's part.)
In one episode of Futari wa Pretty Cure, a boy asked Nagisa out, only to eventually dump her because he'd decided he preferred Cure Black. An unusual case in that Nagisa never actually liked him back, but the same idea.
Inverted in Fresh Pretty Cure! when Miyuki's brother, Daisuke, loves Love instead of her as Cure Peach. When he finds out that Love is Peach, being stupid to confess to her other her about his feelings for the real her, Daisuke tells Love that he will wait for her to tell her feelings to him. However, in the end, she's not going to tell him.
In HeartCatch Pretty Cure!, Tsubomi falls head over heels for a mysterious handsome young man who, later on, resembles her late grandfather when he was younger. Sadly, she's crushed when she comes to find out that he's her grandmother's fairy partner, Coupe.
Tadase in Shugo Chara! likes Amulet Heart, Amu's heroic form. His feelings toward the normal Amu are "just friends". This one is especially weird because he knows from the start that the two are the same person and even tells Amu herself about his confused feelings. Later he confesses that he actually loves Amu for who she is, not her alter ego.
In Code Geass almost all of his love interests have this.
Action Girl Kallen has a Bodyguard Crush on Lelouch's masked identity, Zero, but has a very low opinion of Lelouch, mostly because he cultivates a reputation for being an apatheticjerk. When Kallen dramatically learns Zero's true identity, she gets a Heroic BSOD because taking orders from a classmate is the worst humiliation she could suffer. In season 2, after still going through a "you're Lelouch when I hate you and Zero when I love you." kind of relationship for some time, she comes to love both of them.
Shirley loves Lelouch Lamperouge but hates Zero for killing her father.
C.C. loves Lelouch vi Britannia but sees Zero for the fraud he is.
Misa and Takada, who are not shocked to find out Light is Kira in Death Note.
D.N.Angel has a love triangle revolving around this trope. Daisuke has a crush on Risa, but she rejects him because she wants to date someone "cool". Enter Dark—who is actually Daisuke's alter-ego. Just to make things more complicated, Dark actually has a separate personality and is a big flirt to boot, so Daisuke and Dark sometimes end up in a fight over Risa.
Later on in the manga, this trope is inverted when Daisuke realizes that the one he really loves is actually Risa's twin sister, Riku. Riku cares for him in return, but in a twist, she hates Dark and thinks he's a pervert. This causes all sorts of complications, since Daisuke's family curse won't leave him until he's completely loved for who he is—which includes the part of him that's like Dark.
It's still complicated because Dark is in love with Riku, who's in love with Daisuke. Eventually—in the manga—he begins to reciprocate Risa's feelings, although knowing that they could never be together because he'll disappear once Riku accepts that Dark is a part of Daisuke.
In Princess Tutu, Mytho is enamored with the eponymous Magical Girl, but only considers Ahiru a good friend. (One that he can "tell everything to", but a friend nonetheless.)
A rather peculiar take on this appears in Ai to Yuuki no Pig Girl Tonde Buurin, the main character Karin has a crush on her Junior High School soccer captain Kouichi Mizuno. He is in love with her secret identity Buurin. But she is a pig in that form! Add in the issue of Karin being stuck as Buurin if anyone finds out about her secret identity then you have yourself a very peculiar conundrum. When Kouichi, along with Karin's classmates, finds out that Karin is Buurin, he is upset by this revelation. After fighting his own Demonic Possession, he comes to love her again.
To make things even more ridiculous, Kaede is under the impression that the male Natsuru is her love rival. It turns out she knew it all along because she's the Big Bad. And she really wants only the female Natsuru.
Sailor Moon. In the first anime, Usagi/Sailor Moon loves Mamoru/Tuxedo Mask, while he has a mysterious need to protect Moon. Usagi can't stand Mamoru, who also seems to dislike "Odango Atama". At the same time, he's in love with the mysterious princess of his dreams who is actually Usagi's past self. In the second season, there's also the Tsukikage no Knight, whom Usagi loves while she also loves Mamoru/Mask, though he turns out to be the astral-projected manifestation of Mamoru's love for Usagi when his memories are sealed. The manga is even worse, because Usagi and Mamoru actually like each other there before learning each other's identities.
And Usagi/Serena's little brother Shingo/Sammy idolizes Sailor Moon but can't stand his sister.
Ranma ½ has Kuno hating Ranma, but loves his female side. Inverse for his sister, Kodachi: loves Ranma, but hates his female side.
Inverse variation to Shampoo and Ukyo. Of course, the two find out soon enough.
Mikado loves female Ranma, but hates male Ranma.
Picolet Chardin the 3rd loves female Ranma, but... demands that male Ranma pay his bill for the French food he (Ranma) ate.
Sentaro, Densuke, and Yohyo all love female Ranma (see a trend?) but are rather nonplussed to discover the truth. Sentaro turns vindictive, Densuke tries real hard to forget, and Yohyo is completely flabbergasted and fails to react at all.
For a few episodes of Wedding Peach, Yuri/Angel Lily is confused about her feelings for both Yanagiba and Limone. Guess what the next reveal is.
A strange case in Hayate the Combat Butler, Luca appears to have started to fall for Hayate's alterego, but shows no signs of being a lesbian. She'll probably be relieved to find out that Hayate is actually a guy, though probably unhappy about having to deal with his Unwanted Harem.
Yubisaki Milk Tea first play it straight when Wataru fall in love with Yuki, the alter ego of his best friend Yoshinori, the main protagonist. Later an odd example comes to when Yoshinori realise that he is in love with his OWN alter ego. Both causes a few issues.
Subverted in Wild Rock. Yuuen thinks he's doing a much better job at being a woman than he actually is and assumes Emba's in love with that side of him. He's not.
In Onidere, the female protagonist uses an alter ego to get close to her boyfriend without ruining her reputation as the school's top delinquent and is afraid of losing him to her alter ego, unaware that he figured it out the moment he met her alternate persona.
Inverted in Magical Project S where Hiroto has unrequited love for Misao, but hates Pixy Misa for being a victim of her troubles. Luckily, he gets to find out they're the same person.
Played straight in one episode, where Konoha uses Sasami's baton. She puts Hiroto under a love spell, but he only falls for her transformed self, Funky Connie.
Natsumi from Nicoichi initially fell for the female persona of the protagonist Makoto, not knowing his true identity, which greatly confused her. To complicate matters, Natsumi actually disliked Makoto in his normal self, which created lots of problems for Makoto when he was trying to reciprocate the love.
In Miraculous Ladybug, we've got it twice over. Genki Girl Marinette is in love with the brooding intellectual Adrien, but he can't stand her. However, when he transforms into Black Cat, he's swooning over Ladybug, who snubs him. Ladybug, of course, is Marinette.
In Deadman Wonderland, Ganta was unaware that his beloved Shiro was the true identity of his arch-nemesis, The Red Man. When he finds out, it's not pretty.
Noel in Mint Na Bokurapretends to be a girl to attend the same boarding school as his sister. When he runs into his crush on a day he's not wearing a dress and wig, he tells her that he is "Noel's cousin Tohru". "Tohru" begins dating her. She dumps him when the truth comes out.
In Gekkan Shoujo Nozaki-kun, many guys can't stand Seo, but are in love with 'Lorelei' from the music club... who is Seo, or at least her singing voice; the chief victim of this is Nozaki's junior Wakamatsu. In an inversion, Seo doesn't particularly seem to care either way, and if anything enjoys destroying people's fantasies by revealing who she is.
Lois, to her credit, slapped Clark/Superman when he revealed the deception. Lying isn't nice, Kal-El!
Post-Crisis Lois was initially very skeptical of the Man Of Steel and far more interested in Clark since he was the only person able to routinely scoop her.
Before Clark and Lois got married, there was also the character of Cat Grant, who was in love with Clark Kent and had no particularly personal feelings for Superman (whom she liked and admired in the way most Metropolitans like and admire him.)
In All-Star Superman, Lois never moved past this (which is fitting here because this incarnation thought of himself as Superman and Clark was an act.) To the point where she didn't even believe him when he changed into Superman right in front of her and repeatedly insisted that Clark and Superman were one and the same.
The New 52 reboot gives Lois a new boyfriend, so it seems possible that she doesn't love Clark or Superman anymore.
SometimesLex Luthor does the inverse, respecting Clark Kent a little more than Superman. In some stories they were even friends as kids.
During the Silver Age, a trio of Jimmy Olsen stories (all written by Jerry Siegal) was published depicting Jimmy assuming the identity of "Magi the Magician" and courting a woman named "Sandra Rogers", who was actually his girlfriend Lucy Lane in disguise. While this trope is played straight with Sandra/Lucy, Magi/Jimmy (who was far more invested in his relationship with Lucy than Lucy herself) constantly felt guilt for romancing who he thinks is another woman. A more in-depth look at this can be found here.
Mary Jane, at least for awhile, in some incarnations of Spider-Man. A later Retcon has it that she always knew, but didn't say anything.
More like, always knew but repressed the memory.
Thing is though that Mary Jane really never was portrayed in a situation where she felt attracted by one of Spider-Man's identities but repelled by the other - in the 1960s, when she was generally only involved with Peter Parker, she once used an occasion when Spider-Man rescued her to flirt with him. So the double ID would never have been a romantic obstacle as it was in the case of Betty Brant and Gwen Stacy, who sometimes distrusted and feared Spider-Man (both at one time blaming him for the death of a close relative) or the Black Cat (who disliked Spider-Man's bland civilian alter ego).
Spidey also had the Black Cat/Felicia Hardy. In the comics, this was an inversion: Felicia loved Spidey, and was uninterested in the man beneath the mask. In the cartoon Felicia was in love with Peter, but Black Cat was in love with Spidey. Eventually, Felicia decided not to pursue a relationship with Peter Parker so that her Black Cat persona would be free to be with Spider-Man. In the end, she left with a vampire, and he went with Mary Jane anyway, but it was all very dramatic at the time.
In the comics, the Black Cat was repulsed and disgusted when Spider-Man revealed his identity to her, begging him to put his mask back on. Damn. Worse still, in the Ultimate version of that occurrence, she was so grossed out she vomited on him. (She'd been expecting someone a little older...)
In her defense, the Ultimate Black Cat was a complete inversion of the standard one; she wanted to live a normal life with the man under the mask. The problem being she's an adult (at least in her mid-20's) and he's a 15 year old kid. Definitely a justified squick.
Also, in just about every continuity, Jerk Jock Eugene "Flash" Thompson is a huge fan of Spider-Man and thinks he's the coolest guy on the planet while usually doing whatever he can to make Peter Parker's life miserable.
In some continuities, Aunt May loves her nephew Peter dearly, but can't stand Spider-Man (reasons vary from her thinking he's a dangerous vigilante to her having arachnophobia).
In Silver AgeGreen Lantern, one of the obstacles to Hal Jordan's relationship to Carol Ferris was that she couldn't decide whether she was interested in him or in his alter ego. Eventually she found out that they were the same person, and they moved on to problems like heralter ego.
Wonder Woman's Steve Trevor is a classic example; for decades he ignored bespectacled coworker Diana Prince in favor of her Amazonian alter ego. (After the book's Crisis reboot, this dynamic was disposed of; Diana no longer had a secret identity and her relationship with Steve was non-romantic.)
This is repeatedly inverted with the comic book character Daredevil. Almost all of his female love interests have been looking to date Matt Murdock, not his alter ego. This applies even when the interested party is also a superhero.
Vicki Vale was Batman's Lois Lane (in fact she was a pretty blatant ripoff, being a nosy reporter with an alliterative name and all) throughout the '40s and '50s, but eventually the writers got tired of her and she quietly slipped away into comic-book limbo. She still turns up in The DCU from time to time as a TV reporter, but after the Tim Burton film, she didn't properly turn up again until The Batman versus Dracula (See Rule of Cool).
She's now back at the Gotham Gazette and knows Batman's secret. This results in Bruce recruiting her as an ally.
Daisy Duck frequently plays this role in Disney comics stories involving Paperinik. However, in the stories where she has her own superhero identity (Paperinika, making her Paperinik's Distaff Counterpart) and has to work with the latter, they outright hate each other...
In the Italian miniseries Ultraheroes, which basically is about the founding of a Justice League Disney Comics, Paperinik and Paperinika actually starts to get along, and even falling for each other... which causes them no small amount of angst, since they both already have a significant other - the other's secret identity.
In Flare backup series Sparkplug, this situation is inverted; the superheroine Sparkplug is adored by a local male reporter in both her superhero identity and her civilian identity... because he can tell that they're the same person; He sees Olga and Sparkplug practically every day, a wig isn't going to fool him.
Inverted in Alpha Flight; Aurora is dating teammate Sasquatch, but her alter ego, Jeanne Marie, is horrified by the relationship. (She's a split personality, obviously.)
Several variations of this occur with She-Hulk - originally in Savage She-Hulk, she was dating two guys... one as Jennifer Walters and one as She-Hulk, although that was mutual. Later the trope was inverted when she was married John Jameson who repeatedly expressed a dislike of Jennifer's powered She-Hulk form - much to her chagrin.
Which is a bit hypocritical of her, since she later sated that she didn't like him when his Man-Wolf alter ego.
Ironically averted in The Phantom, the first superhero in comics.
Thundermind of The DCU's Great Ten has this in his secret identity (him being the only member of the team to really have one). In a shameless (and hilarious) riff on Silver Age Superman, Thundermind is also the nebbish, bespectacled schoolteacher Zou Kang. His affections for attractive coworker Ms. Wu are ignored because she only has eyes for Thundermind.
Happens to The Hulk, believe it or not. Betty prefered Bruce Banner, Jarella preferred Hulk and Caiera loves both.
That Betty loved the integrated Hulk shows her consistency; she loved him for his mind rather than his body in all incarnations.
Hilariously inverted in Superlópez: Luisa Lanas (Lois Lane's Expy) loves Juan López but hates Superlópez with a passion.
Adrian Chase, the Vigilante's relationship with Marcia King; she wanted him to renounce the identity of the Vigilante.
The sequel series, Billy Batson and the Magic of Shazam carries on this basic dynamic, but Ret Cons Billy and Captain Marvel into one personality, making it more of a Two-Person Love Triangle.
During the Silver Age, Lana Lang was usually smitten with Superboy, but only thought of Clark as a friend. This stretched into their adulthoods, though she eventually (during the Bronze Age) lost interest in Superman, and even started dating Clark by the late Bronze Age.
In Big Bang Comics, Superman Captain Ersatz Ultiman is really Chris Kelly, but this isn't a secret to his co-workers, because he works for the government in his capacity as Ultiman. However, he keeps another identity on the side: that of his own twin brother, Carl Kelly. "Carl" is a shiftless womanizer, despised by the Ultiman-crazed Lori Lake.
In a large number of Dragon Ball Z fan fics involving Gohan and Videl, Videl almost inevitably falls for Gohan's identity as either The Gold Fighter or as Saiyaman before finding out that they're actually Gohan.
Inverted in the Love Hina/Mahou Sensei Negima! crossover "Four Seasons", with Keitaro asking the net idol Chiu for advice on dealing with his unrequited feelings for a girl...and when she "just out of curiosity" (since unbeknownst to him, they actually know each other) asks the girl's name, he reveals that it is Chisame, her true identity.
In Batman Forever, Dr Chase Meridian first has an obsession with Batman, and then falls in love with Bruce Wayne.
Leading to a FunnyMoment when after Chase breaks up with Batman because she loves Bruce, Batman grins widely once he's out of her sight.
Inverted in, of all places, Death Wish 2. Unusually for a plain clothes adventurer of 1970's and 1980's film, Paul Kersey did in fact maintain a dual identity/alter ego, since the general public did not know that Paul Kersey acted as the vigilante and Kersey continued his work as an architect while acting as a vigilante. In Death Wish 2, Paul Kersey gave an engagement ring to radio announcer Geri Nichols, and they had scheduled their marriage and honeymoon in Acapulco. Nichols did not initially know that Kersey acted as the vigilante, and she strongly opposed the death penalty and unlimited punishment of criminals. When she discovered that Kersey acted as the vigilante, she left the engagement ring behind for him, since his actions as the vigilante clashed with her code of ethics.
Nick: I can feel in my heart that Sheeni is in love with me, not with some fantasy lover in a French romantic novel but me, Nick Twisp. It's funny, after all that, Nick Twisp was enough.
A variation occurs in A Cinderella Story, where Austin falls for Sam whilst in her Cinderella disguise. When he finds out her true identity, he is less than enthusiastic about it. Ultimately averted, as he comes to genuinely love Sam for who she really is.
In Vertigo, Judy loves Scottie but he's too hung up on Madeleine — the dead woman she impersonated as part of Gavin's scheme — for her attempts to make him love her true self work, and she ultimately agrees to be "Madeleine" for him. It doesn't work well for anyone involved.
Even though she knows who he really is, Action Girl/Lancer Elli Quinn from Lois McMaster Bujold's Vorkosigan Saga is deeply in love with her commander, Admiral Miles Naismith—but not so enamored of his real identity Lt. Miles Vorkosigan. ("I've heard you do his accent" is as close as she can come to acknowledging it.) Her refusal to come to terms with this exasperates Miles ("I don't do his accent; he does mine") and eventually scuttles the relationship.
Subverted in Death Sentence (the sequel to Death Wish), Paul Benjamin starts a relationship with a court employee named Irene Evans. Her comments about the vigilante (whom she does not know as just Benjamin's alter ego) do not seem to indicate she particularly supports the vigilante.
Averted in The Spider; Nita Van Sloan supported Richard Wentworth as himself and the Spider.
The Scarlet Pimpernel: Marguerite Blakeney is estranged from her ditzy fop of a husband Sir Percy and in love with the brave, selfless, mysterious vigilante the Scarlet Pimpernel. Talk about some things never change...
This becomes a major problem for Gara Petothel in X-Wing: Wraith Squadron, who is an imperial secret agent who likes her covert identiy as an Alliance pilot so much, she would rather like to become the mask. Unfortunately the one pilot to show romantic interest her is the only survivor of an ambush she had set up months before. Not only did the death of all his friends traumatize him deeply, it's also his friendship to her that slowly helps him to recover.
Live Action TV
Unlike all other adaptions, in Smallville, Lois might be a Hero-Worshipper of The Blur (don't ask why they never used "Superman"), but she is with Clark all the time.
Hannah Montana has Oliver in love with Miley's alter ego, the rockstar Hannah Montana. Of course, he finds out. His reaction: he fainted. Later, Jake undergoes this, only this time, he didn't faint.
Jake: "Jake Ryan doesn't faint, but Leslie, on the other hand, is a little woozy."
A running theme in Lois and Clark was Clark's frustration that Lois never noticed him but swooned over Superman. Much later (after Lois had known for a while and the two of them were married), there was an episode that played with this trope from a different angle: there's a scandal when a tabloid reporter catches Superman in bed with Clark Kent's wife.
In a twist, the show departs from the comics by having Lois deduce Clark's identity before he can propose to her, leaving that uncertainty about what Lois loved about Clark. She does not reveal that she knows until he proposes. This was somewhat settled when he became normal and she got his superpowers for a little while. In the comics, Lois finally fell for Clark then found out about the secret after they were engaged.
Mayson Drake comes at the issue from the opposite angle. She definitely has the hots for Clark Kent, but views Superman as dangerously close to being a vigilante.
Kamen Rider Den-O has an odd variation that relates to Time Travel rather than secret identities. Airi Nogami was engaged to Yuuto Sakurai when he vanished, and interacts with a time-displaced teenage version of him without realizing who he is except she does know, the ignorance is just a front. Airi and the younger Yuuto are never really treated as a potential romance until the end of the series, where the elder Sakurai vanishes into the timestream. The first film of the Chou Den-O Trilogy addresses this further: Yuuto's Battle Butler Deneb ineptly tries to set them up together, before he (and Airi) realize that Yuuto and Sakurai are different people, but the roots of his kind-hearted future self are there and slowly developing, with the ending teasing at what might happen.
On Buffy the Vampire Slayer, Angel is prone to going through a Heel-Face Revolving Door between himself and his evil, soulless identity, Angelus. Interestingly, Drusilla—who's not exactly sane—seems to blame Angel for Angelus' evil actions toward her (torturing him as she recounts them in one episode) even though she loves Angelus. (And of course, this trope also applies to Buffy and Darla, but they don't seem to make the same odd disconnect between the two halves that Drusilla does.)
Though Dru's crazy, so do with that as you will.
On Community Annie gets smitten with Abed whenever he's pretending to be Don Draper / Batman / Han Solo / etc.
In Taxi, Latka's girlfriend Simka returns to New York, but when he tries to declare his love for her, he suddenly turns into Vic Ferrari.
In Help! I'm A Teenage Outlaw. Swiftnick the teenage highwayman's confederates include a girl called Deedee, who he sees as just a friend, if not a total pain who keeps undermining his authority. Meanwhile, he has a hopeless infatuation for Rebellious Princess Lady Devereaux. He has never realised that Deedee is Lady Devereaux in a peasant smock.
During the "Blue Dudes" story arc from Drabble, Norman tries to propose to the girl he's been dating, Norma. She rejects him as she's in love with someone else. He's so crushed that he eventually quits the Blue Dudes in the middle of the next game they attend. At that point, he not only finds out the "someone else" Norma was in love with was his Blue Dudes alter ego, but his previous love, Wendy, was as well.
Older than Television: in the play Cyrano de Bergerac, both Warrior Poet Cyrano and Book Dumb but so very handsome Christian are in love with Roxanne. Since Cyrano thinks he doesn't stand a chance with her anyway because of that big nose issue, he uses his gift for poetry to help Christian woo her so at least he can know they'll both be happy together, which backfires because it tears them both up for years to know Roxanne's really in love with Cyrano but thinks she's in love with Christian. There's also the fact that Christian is killed later and Cyrano stillCannot Spit It Out to not break Roxanne's heart... and keeps denying that the letters are his until his death.
Oscar Wilde's The Importance of Being Earnest has its own version of this, with Jack's ward Cecily falling in love with his alter ego and "Bunbury", Ernest. Not having met him, though, she doesn't know the first thing about him, making it possible for Jack's friend Algernon to pose as Ernest to woo her. Of course, the traditional Loves My Alter Ego is not quite there, but that is somewhat thanks to Algernon who takes on the role of Ernest. Meanwhile, Jack's — who goes by the name Ernest in the city — Love Interest Gwendolyn is convinced that Jack is Ernest, eventually leading Cecily and Gwendolyn to briefly think they're in love with the same man, until it turns out that no one is Ernest.
Polly falls in love with Bobby's "alter ego" in the play "Crazy For You".
In Mega Man Star Force, Luna loves Geo's super hero form, Mega Man, but not Geo himself; after learning that they're the same person, she still claims she only likes Megaman and couldn't care less about Geo. However, she warms up to Geo over time.
The Strangers mod for Freedom Force has one of these. Ordinary doctor Biff Bateman is completely oblivious to the fact that his assistant, Marla Manners, is madly in love with him and tries to talk him into a date/bed constantly. In an attempt to get his attention, Marla takes some of Bateman's shrinking technology along with a taser and a costume she made herself to become The Spider, the beautiful and mysterious crimefighter. Bateman, at about the same time, lets his fascination with other superheroes get the better of him and borrows some experimental military tech to make himself into The Fly, defender of justice. The Fly meets The Spider on the job, and it's love at first sight... for The Fly only, because of a bad first impression. So The Fly dreams about the Spider, who hates his guts, and Marla dreams of Bateman, who doesn't pay attention. Things don't get resolved until they finally learn each other's secret identities.
In Dumbing of Age, Danny explains that he can't date Amber, since he realizes that he was subconsciously attracted to her mainly because of her uncanny resemblance to his ex-girlfriend. Then he explains that he's set his sights on Amazi-Girl instead.
In My Life as a Teenage Robot, Jenny falls for the Silver Shell, a robot suit piloted by Sheldon, who has a crush on her. He originally designed it so that he could act like a jerk and dissuade her from liking robot boys, but instead decided to take advantage of the changing situation.
In Freakazoid!!, Dexter Douglas can't catch a break from the ladies, but they're all over his alter ego Freakazoid. Hell, Freakazoid's girlfriend, Steff, won't even talk to Dex.
Technically, Freakazoid is more of a split personality than an alter ego, which occasionally caused him to actively mock Dexter over this trope. It also meant that when Steff found out the truth, she was at first incredulous, then thought it was funny more than anything else, and never brought it up thereafter.
He actually invokes this trope to get the girl in the first episode. He even acknowledges how shallow it is, but he doesn't care.
Rio from Jem is torn between Jerrica and her secret identity Jem—and he has a bad temper concerning those who deceive him.
Sweet Polly Purebred (practically a Lois Lane Expy anyway) from Underdog.
Similarly, Rosemary the police dispatcher is smitten with Hong Kong Phooey, but couldn't care less about Penrod Pooch.
Playfully inverted in an episode of House of Mouse: Clarabelle accepts a date from Goofy, but in his cluelessness, Goofy believes she turned him down. He later becomes Super Goof and does various heroic acts around the House of Mouse. After he saves Clarabelle from a meteor, he asks her out, but Clarabelle refuses — because she has a date with Goofy.
Similarly, Catwoman loves Batman, but only considers Bruce a friend. He knows both her identities and, according to the "perfect world" illusion created by the Mad Hatter, would marry her, if Batman and Catwoman were out of the equation.
In another animated take on it, Superman: Doomsday, Superman and Lois are actively dating and outright lovers, and he still hasn't revealed his secret identity to her. The normal trope is subverted in that she knows who he really is and makes it clear that she knows; she's just waiting for him to admit to it and stop the pointless denial "for her safety", seeing it as the last blockage of any real commitment between them. He finally does in the last scene.
WordGirl: TJ has a fanboyish obsession with Word Girl that seems to border on a Precocious Crush...but Word Girl is actually his older sister Becky.
However, in one episode where the Botsfords find out Becky is WordGirl, he is mortified and throws away his WordGirl merchandise. He can't get over the fact that someone he looks up to and admires is also someone he considers "ordinary". He even refuses to help her when the entire family is captured by Dr. Two-Brains. In the end, their memories of Becky as WordGirl is erased.
Tobey has a Villainous Crush on Word Girl, but generally treats Becky either indifferently or as an annoying rival. (He sometimes does suspect that they are the same person, though; events just usually conspire to dissuade him of that theory.)
Cybersix: Subverted, Cybersix's civilian alter ego is her crossdressing as Lucas' best friend Adrian. Lucas is in love with Cybersix and vice versa... but then Lucas sees Cybersix go into Adrian's apartment and assumes they're lovers.
Don't forget Lori, a student at the high school who has a pretty open crush on "Adrian," but considers Cybersix to be a tramp (possibly not helped by the fact that she was the one who initially jumped to the "Cybersix/Adrian" conclusion because she tried to see Adrian in his own apartment). And then all is resolved in the final episode, when Cybersix hands Lori "Adrian's" glasses...
It's subtly hinted that Lucas might be bisexual and is also attracted to Adrian, regularly taking "him" out for dinner and at one point even invites him to go see a romantic movie. He even drops everything when Adrian got injured by the monster that turns invisible, sent to hunt down Cybersix, so he can take him to the hospital; and tells him sternly to stop making a fuss when he refused to go to the hospital.
In the Animaniacs short "Moon Over Minerva", Minerva Mink spurns the affections of the nerdy and unsophisticated Wilford Wolf. However, during a full moon, Wilford transforms into a hulking Fabio-esque werewolf, and she immediately falls for him.
Phineas and Ferb plays with this in one episode. Isabella gets annoyed that her usual crush, Phineas, keeps disappearing when she needs him. Meanwhile she swoons over the Beak, the new local superhero, whom she follows around Lois Lane-style. Of course, the Beak is actually Phineas (and his brother, Ferb) in a robotic suit. Genre Savvy Candace calls her out for her Genre Blindness.
Candace: Congratulations, you just earned your "Uh, Durr" Patch.
On Hey Arnold!, Arnold's attraction to Helga (disguised as Arnold's French pen pal Cecile) in the episode "Arnold's Valentine." Helga even soliloquizes about it:
Helga: He likes me. He really likes me! Ohh! (beat) Wait a minute - he doesn't like me, he likes Cecile. Well, not Cecile-Cecile, me-Cecile - so he does like me!. Oh, criminy, I'm a basket case!
The Fairly Oddparents episode where Timmy is "the Masked Magician" may qualify for this—Trixie Tang, who (usually) detests him, finds his eponymous alter-ego to be "a cute superhero!"
Megamind has this with Roxanne falling for the eponymous character impersonating Bernard.
Batman Beyond has a non-romantic version of this trope where Terry's younger brother Matt idolizes the new Batman as Bad Ass and the epitome of cool but sees his own older brother as a boring workaholic who's never around.
Inverted with Terry's relationship with Melanie. Melanie loves Terry, but is lukewarm to antagonistic towards Batman.
Inverted in Phantom 2040: police officer Sagan Cruz has UST with Kit Walker, but sees the Phantom as a glory-hogging jerk. Particularly when he used his "Good Mark" to deface a necklace Kit gave her. (It struck him as appropriate since it already symbolised their friendship, but it hadn't occured to him that it looked like the actions of two seperate people.)
Inverted in American Dragon Jake Long where Rose likes Jake, but hates his dragon form, due to hunting him down. Luckily, she gets to find out they're the same person near the season 1 finale.
A Pepper Ann episode had Pepper Ann become the mascot of her school's field hockey team. While performing in her otter costume, she managed to win over upperclassman Craig Bean. Pepper Ann continued to meet Craig in guise of the otter, but eventually decided to reveal herself to him. Craig subsequently admitted that he knew all along that Pepper Ann was the otter, and also acknowledged how ridiculous it would feel if it turned out he did love Pepper Ann's mascot self more than her.
On Total Drama Revenge Of The Island, Mike's relationship with Zoey is continually impeded by his Split Personality, Vito, having make-out sessions with Anne Maria. Neither girl knows about Mike's condition at first and assumes that the personality they're into is the "true" one and the other is an act.
This has happened to the titular character of Ben 10 on occasion. In the original series, he meets the tetramand female Tiny while as Fourarms, and she immediately starts hitting on him. Luckily, the Omnitrix times out. "Saved by the beep!" Later in the episode, Tiny asks if he'll go back to Fourarms, to which he replies, "Never!"
In Ben 10: Omniverse, Ben turns into an Incursean to infiltrate their fleet, attracting the eye of Princess Attea. Due to the influence of Incursean DNA, Bullfrag(Ben's incursean form) actually starts flirting with her! When all is said and done, Attea offers Ben to join the Incurseans...provided he does so as Bullfrag.
In The Little Mermaid, Eric has vowed to marry the girl who rescued him but since the only thing he clearly remembers about her is her beautiful voice, he assumes that the mute girl he finds on the beach soon after can't possibly be her and is thus reluctant to kiss her even though he's clearly attracted to her from the start. He actually decides after Grimsby's advice that he prefers the flesh-and-blood girl to a "dream girl" who might not even exist, but then Ursula shows up in disguise pretending to be his actual dream girl...
In an episode of Kung Fu Panda: Legends of Awesomeness, Tigress falls in love with the Midnight Stranger who is actually Po in disguise. When Tigress finds out who he really is, she leaves to throw up.