In Den-noh Coil, even the least eye-catching examples of hacking look suspiciously like Hermetic Magic and Instant Runes (the more visual ones? They involved rockets).

It loses credit for abuse of Extreme Graphical Representation, and gains a bit of it back when Yusaku's use of older versions of duel disks and physical cards is an actual hacker technique.

Yu-Gi-Oh! VRAINS gets credit for showing the viewers that the camera is skipping the long, boring hours spent staring at pages of programming language, and enough appropriately used Techno Babble to show that the writers have probably skimmed a programming book.

At one point the access to an important database is hidden inside a duel puzzle arcade machine - the person who thought it up claims that nobody would look for a database there, plus he can slack off at the arcade and claim it's for work. interesting way of shoehorning duels into episodes that otherwise wouldn't have them.

Yu-Gi-Oh! 5D's has a different version rather than passwords, information is hidden behind duel puzzles (a duel-in-progress is presented and you have limited chances to figure out how to win in one turn).

This concept is revisited in Yu-Gi-Oh! ZEXAL, when Yuma's sister Akari attempts to track down and destroy a virus, complete with an RPG-style dungeon and a boss battle.

Said computer also points out how Kaiba seems to be pressing the same keys over and over prompting the latter to claim he learned how to hack by watching old episodes of Star Trek.

Made fun of in Yu-Gi-Oh! The Abridged Series where Kaiba's computer claims to be so advanced it makes hacking look like a boring video game.

In Neon Genesis Evangelion both an Angel and SEELE attempt to hack into the Tokyo-3 MAGI, and both are repelled by Ritsuko's l33t ski11z with accompanying ridiculous graphical representation.

It's almost certainly a parody of this trope, as she uses legitimate hacking techniques (SYN Flood, a Denial-of-Service attack, etc.) that are simply visualized in ridiculous ways (the DOS attack is a tuna, for example), and the 'spells' that she's chanting are Unix shell commands with accurate iptables syntax. A student uses an artifact to transport herself into cyberspace and fight them, Magical Girl-style.

Negima! Magister Negi Magi (the manga, at least) has Chachamaru attempt to hack into the school's computer system, which are represented by pixellated sharks.

In Cowboy Bebop, Ed hacks via a school of cute, tiny fish nibbling on screenshots of web pages.

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