Giant Robo has the remaining members of the Big Bad ruling council, the Magnificent Ten. Plenty of people were disappointed at how they only got a few minutes between them to strut their stuff, but damn it was cool.
They even have the established star thing going for them, as the cast of Giant Robo are all characters from previous anime & manga by Mitsuteru Yokoyama. This was most definitely intentional, as they were supposed to be the main antagonist (as indicated by the Sequel Hook) for the Grand Finale before it got cut short.
Their boss, Big Fire himself, had even less screentime, most of which was actually an impostor, but is just as well-remembered.
A common surprise for anyone that gets into the show via the hype around it is that Internet memeEnsemble Dark Horse Tsuruya has a very small role in the show, with only one or two memorable scenes; her actual Character Focus comes a while later in the books on which the series is based.
Emiri Kimidori, who appeared once in one episode, but got her own Image Song album before some other main characters. She, too, gets fleshed out a little later on in the books, but she's still a very minor character... so far.
Ryoko Asakura could count as well. Sure, she had a few scenes in the first few episodes, and she gets good screen time in The Movie and the tenth novel, but the only scene where she really gets much characterization or interaction with anyone else is a doozy.
Kazuhiko Amagasaki from Tenchi Muyo! who appeared briefly in the first episode of the original OVA series, but ended up with his own Omake comics and a much larger role in Tenchi in Tokyo.
Many fans of Princess Tutu consider a character who only appears in one episode as one of their favorites. Femio, an outlandish, beauty-obsessed, rose-wielding ballet student shows up as a victim for the Dark Magical Girl, and he's so hilarious that he's become a hugely popular character to the fandom, showing up in fanart, fanfic, cosplay and roleplaying nearly as much as the actual main characters of the show, probably because he defeats the powers of darkness through sheer narcissism and stupidity.
Oh yeah, and he's also voiced by Vic Mignogna. Keep in mind that this was years before Ouran.
Gustav St. Germain from Baccano!! fits this trope like a glove. He's in the series for a grand total of ten minutes, barely makes an impact on the plot, and yet he's probably just as memorable as some as the biggest Badasses in the series.
It's also because he's essentially the narrator of the show's Framing Device.
Chiyo's Dad in Azumanga Daioh has a speaking part in about five skits, but is one of the mascots of the series.
Kaworu appeared for only one episode in Neon Genesis Evangelion (and the climactic parts of End of Evangelion), yet he is in the most memorable scene in the entire series and the results of that scene trigger the end of the series (whichever one you go by). It may be interesting to note that he is getting a bigger role in The RemakeRebuild of Evangelion.
Lord Raptor in the Darkstalkers OVA, his depiction is often considered to be incredibly awesome (and is also one of Scott McNeil's coolest performances). Only problem? He was only in the 1st episode for about 10 minutes...
Several one-shot characters in Pokémon apply, even though many of them usually appear in only one episode they are often deemed as some of the show's most memorable characters. Whether its characters whom are actually from the games such as Lt. Surge and Sabrina, or Anime only characters such as A.J and Giselle.
In the TPCI dub, any character-of-the-day voiced by DAN GREEN is likely to be this. Especially Gym Leader Byron.
Death Note: Barring one cameo appearance a few episodes earlier, Matt only shows up for the kidnapping scene before getting riddled with bullets. Hasn't stopped him from becoming one of the fans' favourite characters.
He appears a bit more in the manga before that scene, though his appearances are so sporadic that they all amount to 16 panels note someone counted them maximum.
Then there's TV reporter Koki Tanakabara, who shows up for about one minute to denounce Kira, announcing his full name at the end while knowing that Kira can kill him just by knowing his name and face, and establishing himself as one of the most courageous characters in the entire series.
Burger-kun's five minutes of screentime in Darker Than Black Season 2 somehow managed to net him an internet fandom, for God knows what reason.
Most likely due to his nonchalant attitude and his complaining about having to eat burgers for his remuneration. And he doesn't have the Required Secondary Powers for his Super Speed.
Bruce Ironstaunch from Gurren Lagann. He's just some nameless member of a cheering crowd who makes a Bicep-Polishing Gesture while Rossiu is announcing that Simon will be executed. Since that gesture means "up yours" elsewhere, Western fans saw him as the one good man standing up for the heroes, and he became a legend.
The Farmer with Shotgun from the first episode of Dragon Ball Z.
In Tiger & Bunny, Origami Cyclone is a "superhero" who does very little by way of actual crimefighting, and the ranking system that the city uses places him even lower than the Butt Monkey, Wild Tiger. Nevertheless, his corporate sponsors are very happy with him, because he's good at his real job of inserting himself anywhere there's a camera as living advertisement.
Soul Eater: Excalibur has a tendency to do this, especially in the Wrath Chapter of Eibon.
Shou Tucker of Fullmetal Alchemist is a rather strange example. Even though he's only in one chapter before he's killed off by Scar, he was the first truly intimidating antagonist encountered by the Elric brothers, and still stands out as one of the series' most horrific villains.
In Outlaw Star, Shimi/ Leilong is perhaps the biggest bad ass of the series, defeating the entire crew in open combat, but only appears in one episode, and he doesn't even die like almost every other one-off villian.
Inuyama, the "cowardly" samurai/firefly enthusiast/ assassin from Samurai Champloo only gets one episode and he nearly beats Jin, stopping only when he discovers his employer's death and decides to walk away. And what's worse, he promises that they'll meet again.
Code Geass has Mao. He was only in a few episodes in a row towards the middle of the first season, but is remembered for being Crazy Awesome, and at the very least foreshadowed Lelouch's Power Incontinence.
Robotech: The Macross character on which Dr. Emil Lang was based on was just an unnamed chief engineer in the original Japanese version. The character design already had cool looking all black eyes. Robotech went further gave Dr. Lang a memorable German accent (courtesy of actor Greg Snegoff). All this for a character that had only appeared in two episodes with three minutes total of screen time. He would become a major supporting character in the aborted Sentinels production and the rest of the Expanded Universe.
Kimihiro Watanuki made a 14-minute appearance in Blood-C: The Last Dark where he provided Saya's sword which would use to kill Fumito. He brought out about the price for the sword which Saya mentions that she would do it later. By the end of the movie, this was not mentioned again and the sword is left behind after Saya killed Fumito.
This goes the same with Yuka Amino, the 28-year old woman who pretended to be Saya's friend in the TV series and wanted to be the governor of Tokyo. She only has two scenes where she does secretarial duties for Fumito and by the end of the movie where she finally achieves her goal as governor without any repercussions.
The first Shuffle Alliance in Mobile Fighter G Gundam. Their absurd Gundams transform from playing card suits—diamond, spade, etc—and they themselves are a pretty flashy bunch of Badasses in Awesome Anachronistic Apparel who take out a bunch of DG-cell-infected, subway-car-throwing Gundam Fighters hardly breaking a sweat. And they're a match for Master Asia. Sad, then, that they do a collective Heroic Sacrifice to save the new Shuffle Alliance in just the next episode.
If this trope can be played negatively, MaloMyotismon would qualify (putting aside his previous incarnations as Myotismon and VenomMyotismon). He only appeared during the last two episodes of Digimon's second season, and is remembered as one of the suckiest villains ever in an anime series.