When 80's Leonardo is explaining how they ended up in the 2003 universe, he said "Don had this rocking idea." The turtles were never addressed by their nicknames in the 80's cartoon.
The 80's Shredder called his 2003 counterpart a "pink slug." While it is true that most Utroms are pink, the Utrom Shredder is red.
Shredder from the original cartoon planned to use the Giggle Ray, an invention featured in "Raphael Knocks 'Em Dead," but the said invention was implemented by Barney Stockman, not Shredder and Krang.
The exploding throwing stars were first used in the "original series" episode "Return of the Technodrome."
The fly that was accidentally mutated before the 2003 Turtles rescues their 1987 counterparts, might be a possible nod to the 1987 Baxter Stockman.
Donatello was unable to zoom in on a clear image of the 1987 Turtles but he was able to zoom in on the Purple Dragons.
It should be noted that Channel 6 is referenced for the second time (the first time being the second season episode Secret Origin's, Part 3) in this show. This happens when Master Splinter's soap opera is interrupted for a news bulletin.
When the Turtles teleport themselves into the 1980's Turtles dimension, we can see that Irma Langinstein makes a silent cameo in the movie, as one of the persons passing on the street.
Among the Multiverse of TMNT the 2003 Shredder revealed are the Turtles from the movie series, the Turtles of the future Donatello went to in "Same As It Never Was," and the Super Turtles Michaelangelo met in "Reality Check."
Karai is working for the Shredder again but in "Wedding Bells and Bytes" she was seen as a guest at Casey and April's wedding.
The device Bebop and Raocksteady used to find the Turtles' lair was used in the original series' episode "Beware of Lotus Blossom."
Shredder (1987) claims that there is no Krang in this universe when he does a dimensional scan. However, there was a short mention of a Krang in "Secret Origins, Part 3." This was probably a forgotten line of homage dialogue.
Cyber-Shredder appears to be gone for good, however, based on the future the Turtles witnessed in Tempus Fugit, he (along with the Utrom Shredder and Tengu Shredder) may return.
Although in that future Khan said he destroyed the turtles, which never occurred, showing that the timeline can change. But it could also mean that he destroys them at some point after "Wedding Bells and Bytes."
In the scene where the cape is stolen, Action Comics #1 can be seen behind the cape's owner.
The technique Michaelangelo uses to defeat Cyber-Shredder in the same technique Splinter used to defeat the Utrom Shredder in The Shredder Strikes, Part Two.
Hun and Baxter are working together despite the fact that they hate each other.
If there's been a engram of the Shredder all this time, why didn't the Foot activate it after he was banished?
At one point, the turtles arrived at what appeared to be a future event in which the original Tengu Shredder (who somehow came back to life), Ch'rell, the Utrom Shredder (who somehow returned from his exile), and the new Cyber Shredder are having a three-way war. In addition, the turtles encounter a strange warrior who claims to have defeated them.
When Mikey says he'll call the triceratops Zog The Second, he's making a reference to the other Triceratops he befriended in Return Of Savanti.
Falcon was the name of the Planet Racer Raph teamed up with in Across The Universe who looks just like the Falcon in this episode, only older.