Daisy

Daisy was the Doomguy's pet rabbit. The rabbit's head is shown in the end picture of Episode 3: Inferno, impaled on a pike as evidence that the hellspawn have come to Earth, but the rabbit is not specifically identified as the Doomguy's pet.

In the end picture of Episode 4: Thy Flesh Consumed, the rabbit's head reappears in the Doomguy's hand. The preceding text mentions that "someone was gonna pay for what happened to Daisy, your pet rabbit." Due to the lack of any previous mention of this in the Episode 3 text, this would appear to be an example of.

The original episode 3 ending sequence does not appear in most console ports of Doom. In the Game Boy Advance port, the ending of episode 4 is uniquely displayed instead, even though that port contains no other resources from Ultimate Doom.

Doom (2016)
Daisy is referenced off-hand in an Easter egg in Doom (2016), where a poster on a wall in one of the multiplayer levels features a generic picture of a rabbit with the caption "REWARD - Lost pet rabbit Daisy", and instructions that if she is found, the fake phone number 121-019-93 should be called, which is also in turn a reference to Doom's original of December 10, 1993.

Quake Champions
id Software's game  features the Doom Slayer as a playable character. Each playable character in the game possesses an artifact item as one of their collectable lore entries. For the Doom Slayer, this artifact is the left hind foot of his pet rabbit Daisy, whom the game states was "killed by marauding demons when their invasion of Earth began." The presence of this artifact and its attachment to the Doom Slayer character is cited by many as additional evidence that id Software may consider the character to be one and the same person as the original Doomguy.

Doom Eternal (2020)
Daisy makes a small cameo appearance on the full cover art for Doom Eternal. She is seen on the far right hand side of the image running away.

In the Fortress of Doom, a portrait of the Doom Slayer holding Daisy, as well as her cage and a bag of rabbit food can be found.

On January 21, 2020, Hugo Martin confirmed that a hidden bunny would be a featured secret in every level of Doom Eternal.

Unofficial

 * Daisy makes an appearance in Action Doom in the final level, which takes place at Deimos due to unforeseen events that took place at the "Union Aerospace Laboratory". She is animated, and runs around Doomguy's base in space; the player cannot harm Daisy in any way.
 * She also appears as a cheat skin of past versions of Skulltag.
 * Daisy can also be seen alive on the start-up screen of the Doom95 port.
 * Her severed head is the default mouse cursor in ZDoom when running Doom games.
 * The IWAD for Chex Quest contains all the original Doom ending images, including the impaled rabbit, though the images are never shown to the player in the actual game. This would be rather graphic content for what is otherwise a family-friendly game.

Trivia

 * Many players perceive the pike as being an arm holding up the head, due to its flesh-like coloration. The most common interpretation is that it is the Doomguy's hand, since he is later seen with it in the ending to Thy Flesh Consumed.
 * The 2019 motion picture Doom: Annihilation contains two different references to Daisy. The first is in the form of the resident AI of the armored transport ship Nola, which is named Daisy, and the second is the lucky rabbit's foot carried by the ship's pilot, Morgan.