When you play in the campaign, in the Venom team, two of the characters are named Ada and Lovelace, named after the first woman programmer in the world.
One of the Female Commando (Dark Phalanx) characters is called Nikita.
One of Xan Kriegor's quotes is "I am the Alpha and the Omega". The phrase is also used as the description for the "Godlike" difficulty that practice bots can be set to.
Gorge's team, their suit, and their name (Juggernauts), are shout-outs to The Juggernaut from X-Men.
The Bridge of Fate maps (one for Bombing Run, one for Capture The Flag) are modelled after an environment from The Lord of the Rings (more precisely, from the movies).
One of Devastation's adrenaline combos, "Head Turret", has her activating mounted turret defenses, not unlike those of Fulgore'sNo Mercy.
Many of her Ladder challenges have references to programming concepts. One of her matches is labeled "GOTO: Next Match", and the description of another match has a C++ fragment.
One of Raiden's ladder challenges has a reference to the Netherrealm, stating that he hates to use their powers, but in order to advance in the Tournament, he must do so.
Some of his taunts are, obviously, references to Mortal Kombat:
The challenge where he's unlocked is called "Unreal Kombat 2". A previous challenge where Anubis faces both Malcolm and Raiden is called "Unreal Kombat".
A challenge where the player has to defeat two Raidens mentions the Elder Gods.
Outside of MK references, one of his Ladder challenges pits him against the Skaarj Torgr and the human female Sappire. The match is called "Beauty and the Beast".
One of Raptor's challenges is named "Carnage++", a reference to the C++ programming language.
The Greed gametype is inspired in the Greed mod for Unreal Tournament 2004 which in turn is based on Quake III: Team Arena's Harvester gametype. Given that the UT2004 mod replaces the skulls of Harvester with coins and the UT3 gametype brings the skulls back, it's possible that UT3!Greed is a mix of both.