Kraang (Teenage Mutant Ninja Turtles 2012 TV series)
The Titan (Titan A.E.)
GOD (Toriko); via food memories
Omnitrix (Ben 10)
Petropia Back-up Crystal (Ben 10: Alien Force)
Nemetrix (Ben 10: Omniverse)
Growth Codex (DC Extended Universe)
Control Medal (Guyver)
Lawgivers (Judge Dredd)
Phantom Ruby prototypes (Sonic Forces)
Dual Trace System (Trace Memory)
Primus (Ben 10 series); via Codon Stream.
The Omnitrix (Ben 10) contains the DNA of virtually every alien species in existence.
Primus (Ben 10) contains the Codon Stream, which acts as a DNA database for every sapient species in the universe.
The Petropia Back-up Crystal (Ben 10) has the collective DNA of the entire Petrosapien race, allowing it to resurrect the entire species from extinction.
Slimebiotes (Ben 10: Omniverse) gather, carry, and mix DNA to deposit it on planets.
Lavos (Chrono Trigger) contains the DNA of every life form that has ever lived within its body.
The Joker (DC Animated Universe) encoded his DNA into a microchip that he implanted into Tim Drake's spinal cord, allowing the Clown Prince of Crimes to slowly but surely "reborn" in Drake's body.
The Growth Codex (DC Extended Universe) contains the genetic information of every individual Kryptonian...
...and is currently housed within the body of Superman.
Baby (Dragon Ball GT) possesses the genetic information of the Tuffles, making him a DNA archive for their race.
Dr. Gero's remote tracking devices (Dragon Ball Z) are specifically designed to record and store the DNA of Goku and the Z-Fighters for the creation of Cell.
The Guyver's (Guyver) Control Medal stores its host's DNA, so that if the host is injured or killed, it regenerates that host from even the smallest bits of genetic material.
The Librarian (Halo) documented and indexed the DNA of various sentient species to prevent them from being consumed by the Flood.
As part of their unique reproduction, Chimera Ant Queens (Hunter x Hunter) incorporate the DNA of whatever they consume and pass those traits on to the next generation of Chimera Ants.
After becoming the Ultimate Life Form, Kars (JoJo's Bizarre Adventure) contains the DNA of every organism to ever live on Earth within his body.
Lawgivers (Judge Dredd) encode the DNA of the Judge authorized to use them, ensuring that only the authorized Judge can wield them without the gun exploding in their hands.
Morlun (Marvel Comics) contains the DNA of animals, birds, humans, and insects within his body, forcing him to feed on totemistic superhumans to replenish them.
Mew (Pokémon) contains the DNA of every single Pokémon species within its body.
The Phantom Ruby prototypes (Sonic Forces) record the DNA of the first person who triggers them; thus, only that person can activate and use them.
Spider-Man 2099 (Spider-Man: Edge of Time) using DNA stored in Alchemax's database to establish a chronal link with the Amazing Spider-Man.
Spider-Man (Spider-Man: Edge of Time) using a DNA recorder to collect the Atrocity's DNA...
...and upload it into Alchemax's database.
Under the cover of the Worldwide Genome Project, the Kraang (Teenage Mutant Ninja Turtles 2012) have collected and stored the DNA of every animal species on Earth.
GOD (Toriko) has stored the DNA of every living thing that has existed since life began in the form of Food Memories, which is the main reason its almost impossible to prepare as a dish without dying from fatigue.
The Dual Trace System (Trace Memory) encoded the DNA and biometric data of Ashley Robbins, ensuring that only she can use it.