Nerd glasses time:

My Buddy Superfly- Daikatana reference (and maybe John Romero in general).

Why I'm So Great pt II- Obviously Duke Nukem but they can't use his real name due to Randy bo-Bandy owning the Duke Nukem IP.

Devilish Daggers- Devil Daggers, an indie hoard shooter inspired by older games like Doom.

Liandri- Unreal, though more so Unreal 2 and the Tournament games.

Von Braun- System Shock 2

Mesa Science Monthly- Half-Life

U-NAT-CO Training Manual- Deus Ex (and a little joke to the famous "a bomb?!" scene)

Spear of Destiny- Wolfenstein 3D (was the name of the expansion to Wolf 3D)

Living with Rage- RAGE series

The Strogg- Quake 2 and 4

Ret-conned- the Doom novels which called Doomguy "Flynn Taggart"

Nopefish to Dopefish- The dopefish from Commander Keen

Tei Tenga- Oh that's a deep pull, it's a reference to the alpha of Doom 1 and when it was originally going to have adventure game elements and be set on a fictional place called Tei Tenga (though the name Tei Tenga stayed in the final game on some computer monitors as a left over texture)

Thy Flesh Consumed- The 4th Doom 1 episode that was added to the Ultimate Doom re-release in 1995

2 Prey or Not 2 Prey- Prey franchise, might also be a somewhat twisted joke on how Prey 2 was scrapped but Bethesda told Arkane "hey that sci-fi immersive sim you're making? Just call it Prey, we own the rights to the name"

Vault Dweller's Sirvival Guide and Nuka-Cola- Both are of course Fallout references.