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While the Scott Pilgrim universe has primarily a video game influence, the graphic novel also tends to reference manga and anime as well.

In Precious Little LifeEdit

On the side of a bus as early as Volume One, there is an ad for Trapnest's new album, Trigger. This is a direct reference to a famous band within Nana, whose latest album was called Trigger.
When a character is introduced, a small box appears with their name, age, and other weird information. This happens in some manga.
The art style is reminiscent of manga style artwork.

When Todd uses his vegan powers, his hair flows upward and he glows in a way similar to a Super Saiyan from the Dragon Ball series.
While the appearance when Todd uses his powers change references Dragonball Z, his display of putting holes in the moon is another Akira reference, along with Ramona describing the aftermath as "thirty pages of explosions and tidal waves". In Akira Tetsuo displays his psychic power in this manner.
In Dragonball Z, most of the names of Saiyans, are related to vegetables, and that has a clear reference in Todd's "vegan powers"
In Volume Three when Ramona takes out her hammer she yells "Believe it!". This is what replaces Naruto's original catch phrase "dettebayo" in the English dubs when the anime was brought to North America.
On Chapter 14, the chapter name references the movie tag of the Japanese animation Akira.
One of the posters in Envy and Julie's dorm room is the popular Studio Ghilbi film Porco Rosso.

Scott describes his Zelda-esque dream sequences as "cool. Like anime."
The page at the back of volume has a warning telling people that they've started at the wrong end of the book. This is a reference to many Manga books that are published outside of Japan, as literature in Japan is read from right to left (as opposed to left to right), Manga books often have warnings at the back of the books (what would normally be the front for western readers) telling them they've started at the wrong end.
Scott performs a "Diagonal Cut" to defeat Roxie, a move common in anime and manga.
Roxie, just by being a half-ninja, references many ninja manga

Upon leveling up, Scott's drawing of the Power of Love and also the Power of Understanding from his chest is similar to how Utena draws her Sword of Dios from Anthy's chest before a duel, as seen in Revolutionary Girl Utena.
Despite being compared to Cloud's Buster Sword, Power of Understanding is closer in design to the shikai form of Ichigo's Zanpakutō (soul-cutter sword), Zangetsu, from Bleach, this is also an inderect reference to the Tessaiga from the InuYasha series, as Zanpakutō are based off the Tessaiga.
Gideon's look is similar to stereotypical anime and manga antagonists where they have glasses, in many ways possible.
On page 39 there is a picture of the straw hat crew's ship the "Going Merry" from the anime and manga One Piece behind Scott.
Gideon unleashing The Glow looks somewhat similar to the Kamehameha Wave from the Dragon Ball series.
On page 49, the appearance of Gideon the Cat while on top of Scott's dresser is similar to "Kuroneko-sama/Lord Black Cat" from the Trigun anime and manga series.

He is also seen wearing a shirt with the guitar symbol from rock band on his shirt when he is fighting Ken and Kyle.

Also in the film adaptation, Envy Adams' look and outfit is reminiscent of Misa Amane from Death Note; a manga which Bryan Lee O'Malley is a fan of.
The Deveganizing ray resembles the Spirit Gun from Yu Yu Hakusho, moreso in the movie
In The Film, Gideon uses hand seals like Naruto to summon his Katana.
The inner monologuing Scott does when seeing Knives talking to Ramona is common in Anime shows.
The 5 way split of everyone gasping over Scott's death is also common in Anime.