Okies I'll post all the stuff I know about. I'm pretty sure all this is pretty well known by most who've played the games but whatevers! I'll leave it up ta someone else to sort out which is a "secret" and which is "easter eggs".
In each game on servers other than Delta you can look up at the sky in some areas an see stuff flying around up there related to bonus dungeons. However Quarantine's has no dungeon relation. Instead its sky high thing is in relation to around when the game takes place, namely Christmas! In snowy fields such as Ω Bursting Passed Over Holy Ground you can enter first person an look around to see Santa?! His sleigh being puled by a pair of Grunties with antlers lol. Here's a screenshot I took not to long ago: http://i1.minus.com/ibakOGs8HEQZg0.jpg
Someone with better quality capture stuff could surely get a much better look.
Each server has a designated color!
Δ (Delta): Red | Θ (Theta): Blue | Λ (Lambda): Green | Σ (Sigma): Yellow | Ω: Light Blue
You can see the server name in said color in the upper right part of the screen when entering a server/area.
All Grunties have horns. Not physically on their bodies, but if you take a look at their shadows...
When you make it into the Top 5 of the Hero of Zeit ranking, the "Hero of Zeit Ranking" post on the board actually updates to include you and your time! This might go unnoticed by many because "new" isn't displayed on the board after this change takes place (cause its a post edit instead of a new post I guess).
The banner ad in the web news changes with each game.
Infection: Tail Concerto
Mutation: Tail Concerto 2
Outbreak: Silent Bomber
Quarantine: Silent Bomber (different image)
Similarly, the Login screen changes with each game.
The rare Wavemaster weapon Silent Bomber is an obvious shoutout to Silent Bomber. It grants a summon called "Stuck?" which makes no sense to me but the summon itself is unique and I guess maybe a reference to? Find the Christmas Card item at Ω Reincarnated Elusive Lyric Poet then trade it to the Silent Bomber named PC Jutah.
The following items found in Outbreak are all meant to be traded to PCs with Tail Concerto connections for rare equipment. The items themselves may be references but I never played that game, so idk.
Σ Noisy Sacred Ringing Ears - 3 Floor Tower - trade to: Alicia
Σ Barking Hot-Blooded 500 Lohan - Magnolia Miso - trade to: Flare
Σ Unusual Ghostly Remnant - Doll Amulet - trade to: Stare
Σ Ancient Destroyer's Battlefield - Scent of Gero - trade to: Fool
Σ Tested Morphean Alchemy - Field's Deed - trade to: Waffle
Σ Entwined Prejudiced Chaos - Rouge Fragment - trade to: Cyan
Σ Abrasive False Tragedy - Maiden's Plot - trade to: Teria
Equipping the Cats Blade, Cats Hat, Cats Mail, Cats Gloves, and Cats Boots to any Twin Blade grants 'em a summon called "Meooow" and I guess is a reference to Tail Concerto. Cats Blades can be found in Infection, but the rest of the set is found in Outbreak.
This ones another Outbreak item but oddly its traded to a Silent Bomber character named PC.
Σ Greedy Gambler's Drift - Boxed Lunch - trade to: Benoit
Prolly since the 8th Tail Concerto character named PC was taken since Infection.
Δ Hideous Organ Market Scaffold - Ice Bar - trade to: Panta
The item "BL Yokohama" found in the Mutation dungeon Λ Bottomless Soul Kaleidoscope seems ta be a reference to Blue Light Yokohama which is either a song or a restuarant or both!
The rare Wavemaster weapon "Yoshida (26)" (gotten from the Boxed Lunch trade above) could be a reference to the Yoshida Fire Festival which starts on August 26th. Could also be a clue as to when the events of Liminality Vol.3 takes place.
The "Bent Glasses" found in the Mutation dungeon Λ Lightless Sacred Remains could be referencing the fate of Yuki's glasses (main girl of Liminality Vol.2).
And the "Risky Coffee" item found in Quarantine dungeon Ω Sickened Imprisoned Fallen Angel is an obvious call out to scene in Liminality Vol.4 where Yuki sets off an alarm while on a coffee run.
The rare weapon "Bom-Ba-Ye" could be a shout out to an old japanese wrestler. Obtainable by Data Draining a "Mu Guardian" in any of the games. Δ Hideous Someone's Giant is an early place ya can find one.
Simple lists of TC / SB named PCs~
TC: Alicia, Stare, Flare, Fool, Teria, Waffle, Cyan, Panta
SB: Jutah, Annri, Benoit, John, Micino, Tim