The Icon of Sin is a wall decoration in several levels such as "Dueling Keeps".
Anarki has the Lost Soul on his skateboard.
The back of Biker's jacket has a demonic head in a pentagram.
The Rocket Jumping tutorial map in Live has the Red Keycard as an Easter Egg.
The UAC logo appears on the map forgotten ("The Forgotten Place" in III) in Live.
The BFG functions as it was originally intended in Doom, except that version wreaked havoc on the hardware, slowing the framerate to an absolute crawl and making the screen look like Christmas.
The Crusaders from Team Arena are clearly inspired by the Heretic and Hexen games, particularly the Crusader class from Hexen II, which id Software published.
The challenges "Military Mayhem" and especially "Generations" in Arena Arcade pits you against former main characters Doom, Ranger, Bitterman, Grunt and Stripe.
Several of the map names for Arena Arcade are taken from Quake Live such as "Chemical Reaction"note Q3A's "Deva Station", "Cobalt Station"note Q3A's "The Bouncy Map", "Rebound"note Q3TA's "Capture Chamber" and "Beyond Reality"note Q3A's "The Very End Of You".