500 Manga Creatures, a book that purported to provide manga clipart, might as well have been named "300 Manga Creatures Plus 200 Potential Lawsuits from Game Freak" thanks to its inclusion of somewhat obvious examples of this trope applied to the Pokémon franchise. Kyogre, Dratini, Dragonair, Zapdos, Shuckle, Metang, Metagross, Shroomish, Swablu, and Bagon are just the most blatantly obvious ones.
Actually acknowledged in the book's description, where it claims that the characters include "Digimor (sic) and Pokémon-style creatures", among others.
Angel Beats! has Yuri, who looks like a color swapped Haruhi from The Melancholy of Haruhi Suzumiya, only with straight bangs. She leads a group of students with a similar name to the group of students that Haruhi leads (SSS vs SOS) and even acts somewhat like her. Their backgrounds and goals are different, but their characters are pretty much the same otherwise. At least, initially.
Angel BladeH-series has a few characters that may be pretty familiar to some people, but the most-definitely-not-Kekko Kamen heroine is the most obvious example. Justified since AB is basically a parody of Kekko Kamen.
At least two characters are CEs of Mai Shiranui (the director apparently includes one in every project he works on as a Shout-Out, two more are basically the lead females of Gowcaizer renamed, and one more is Mizuki from Gravion given the same treatment.
Bleach has one of the most famous Captain Ersatz, Orihime Inoue: Ushio and Tora's Mayuko is probably her long-lost twin sister. Shy and naive behaviour? Check. Second female lead? Check. Amazing supernatural barrier-creating and healing powers? Check. They even share the same freaking surname.
CLANNAD's Fujibayashi sisters and Lucky Star's Hiiragi sisters. Both pairs are twins, both have purple hair, the elder twin is a tsundere, the younger twin is quiet and reserved, they sport Tsurime and Tareme respectively, both twins' hairstyles resemble their Ersatz counterpart's... Seriously.
There is one notable difference between these two pairs of twins when it comes to Feminine Women Can Cook: The Hiiragi twins play it straight. Tsukasa is a very good chef and is among the only things where her Dojikko tendencies do not show, and Konata often teases Kagami about her cooking. However, the Fujibayashi sistersinvert this concept. Ryou's cooking, although it looks good, makes Botan faint in disgust while Kyou's food is great to the point where Tomoya is honest about how good it is.
Keroro Gunsou has, among others, Baio and Ouka Nishizawa, whose younger selves are heavily based on Ryu and Chun-Li from Street Fighter, although in the present their lives are radically different.
Other examples Eddy Honda, one of Ouka's opponents in her street fighting days, to Edmond Honda from Street Fighter II; a monster called "Ningen", with appearance and background nearly identical to Adam from Neon Genesis Evangelion and an unnamed alien judge who looked identical to the judge from Phoenix Wright, save for green skin and an antenna on his forehead.
Gintama featured a large number of Captain Ersatzes throughout the series, most used for short parody scenes, like the intergalactic emperor Breeza, obviously a parody of Freeza from Dragon Ball Z or the old man from the lake, the spirit of Gintoki's sword, who looked pretty much like a red version of the human form of the sword of Bleach's protagonist, Ichigo.
Princess Lover has Sylvia van Hossen, who is almost a complete clone of Saber of Fate/stay night. Even to the point where several fans thought it was her until she was named. The only difference between them seems to be their backstory and Sylvia's much bigger breasts.
Tenchi Muyo GXP has Seiryo Tennan and Amane Kaunaq who are a Shout-Out to Tatewaki Kuno and Akane Tendo of Ranma ½, including the obsessive stalker-violent tomboy childhood "relationship" to one another.
In the obscure 1960's Batman manga, Go Go the Magician is Flash villain Weather Wizard, just with a different name. This is probably due to the fact that the artist had been given some Batman comics and been told to adapt them into a Japanese style - evidently one of the issues was Detective Comics #353, where Weather Wizard bedeviled Batman for a change. The reason for the name change is a little fuzzy, though. Maybe Weather Wizard's stylin' outfit gave the impression of him being one hip swinger, Clyde?
Since the distinction between copyright free monsters and Dungeons & Dragons originals would remain obscure to laymen for several more years, Bastard!!'s manga originally featured a Beholder. After getting complaints from TSR's Japanese division the comic's supervisor Mr. Suzuki profusely apologized. The monster was slightly altered with comical arms and legs and renamed the "Suzuki Dogezaemon" for the collected volume. Dogeza meaning "apologizing on hands and knees," the incident gained some entertaining notoriety.
Konami would reference this in their Castlevania games with their own mock-Beholder, the Dogether.
Dragon's Crown has its own stand-in, the Gazer. It may be yet another phonetic nod to the joke.
Early translations of Lupin III had to change the main character into an Ersatz because the original author had never asked permission to create a character based on Arsčne Lupin. He would be called "Rupan" or "Wolf" or, in the French version, "Edgar of Burglary."
In a Continuity Nod to the original Lupin's Captain Ersatz, Lupin III was forced to face off against "Herlock Sholmes III."
Lost Brain has Rei Hiyama, a top student, bored with the world who comes upon a power of some kind and uses it to control and kill people in order to create what he considers an Utopia, where his will is the law. Also ends up playing Xanatos Speed Chess against an opposing Chessmaster who is leading the effort to catch him. Very similar to Death Note's Light Yagami.