Actor Allusion: Peko is voiced by Kotono Mitsuishi, AKA Sailor Moon. When she masquerades as Sparkiling Justice, she wears a Magical Girl mask that greatly resembles Sailor Moon and makes a speech about punishing people with justice. Since Mitsuishi was one of the voice actors that the script writer specifically asked for, this was most likely done intentionally.
In the English dub, Hajime is voiced by Johnny Yong Bosch, who voiced Yu Narukami in Persona 4; fitting, since both games revolve around finding the truth. However, he also voiced Tohru Adachi, the seemingly-harmless cop who is driven by his envy and misanthropy to try destroying the world. Sounds an awful lot like pre-amnesia Hajime and Izuru Kamukura, doesn't it?
Another English dub example: A pink haired girl with matching pink eyes who sacrifices herself in the name of hope for her friends, but did not really die so much as she is nonexistent in the real world. Madoka Kaname... or Chiaki Nanami?
A third English dub example (and a two-for-one deal, too): A boy is trapped in a virtual world gone horribly wrong. Kirito... or Nagito Komaeda? Later, a boy specifically enters the virtual world to save those trapped in it. Again, Kirito... or Makoto Naegi?
Acting for Two: Nagito's voice actors in both the Japanese and English versions also voiced Makoto from the previous game. It falls into this trope when Makoto shows up. There's also Akira Ishida and Jason Wishnov, who both voiced Byakuya in the previous game and again here. It falls into this trope considering that the Byakuya we meet here is an impostor, and the real one shows up later.
Fan Nickname: Byakuya as he appears in this game is known by fans as "Fat Togami" or "Fatgami", due to how...different he looks from when we last saw him. "Twogami" and "2gami" are also popular, given how he's someone completely different from the actual Byakuya. In this vein "Fauxgami" is also a common name English speakers use when spoilers aren't considered an issue. In Japan, "Tongami" is a very popular nickname for him.
Monobear can be considered one too since his official name is still Monokuma.
Due to its status as a Walking Spoiler, Izuru Kamukura is being affectionately referred to as "Spoiler-kun".
As far as other Bleach characters go: Akane is also Yoruichi Shihouin, Mikan is also Isane Kotetsu, Nekomaru is Isshin Kurosaki and the replacement Kenpachi, Kazuichi is Sousuke Aizen and Ganju Shiba, and Ibuki is Jackie Tristan (among other minor characters).
Nagito originally had glasses, and a hoodie with bat ears that eventually became Chiaki's.
Chiaki greatly resembled Chihiro, the person who made her.
Fuyuhiko's prototype, of a big, muscular man, eventually became Nekomaru's design proper. Nekomaru's original was much more standard, with no crazy muscles.
Teruteru was a standard tall and slender Bishounen.
Mikan had shorter hair and more of a Mad Scientist vibe, being covered in stitches (in fact, one sketch has her hand falling off at the wrist) while carrying around a Brain in a Jar.
One of Nekomaru's early designs was a Long-Haired Pretty Boy. Another was done in the more cartoonish style that was ultimately used for Teruteru, depicting him as a rail-thin teenager with a shaved bald head, oval eyes and buck teeth.
Hiyoko was one of the survivors while Fuyuhiko was the victim of the third chapter in the beta version of the game.
Characters who serve as gods in the Trope Pantheon: