When Bill says "Lock up those two Jews" he was refering to Kyle and Jesus, but how did he know Kyle was Jewish?
Stan saying to Jesus that "we haven't talked in a long time" is an in – joke referring to the fact that Jesus hasn't appeared on the show since season 6.
When Jesus uses the bladed throwing star to kill the villian false Pope Bill Donohue, this references what happened in the very very first existence of South Park titled "The Spirit of Xmas" but also misknown as Frosty versus Santa (misknown because Frosty is an evil monster who only pretends to be Santa but the actually title should be Frosty versus Baby Jesus) which was the very first Spirit of Xmas and fully hand drawn by Matt and Trey while in film school. This version preceded the later version also titled The "Spirit of Xmas" but which was done with the cardboard (like the first series of South Park episodes were created) and featured a fully grown Jesus battling Santa.
In this very first original short the boys Stan and Kyle pray for Jesus to appear to save them from the Frosty monster (another allusion to Stan praying for Jesus to appear and save them in the Easter episode) and the baby Jesus appears out of the manger but with a full beard just as the fully grown Jesus has in the Easter Episode. The baby Jesus takes the halo from off his head and throws it a distance just like Jesus throws the throwing star in the Easter Episode and this cuts through and kills the evil Frosty monster. Again this is also an allusion that Jesus' halo is substantial as when in the Easter special when Jesus dies in the cell after Kyle stabs him his halo falls to the floor and makes a ringing sound like it is solid and metal.
In this episode it is said that Saint Peter was a rabbit. However in the season 9 episode "Best Friends Forever" when Kenny went to Heaven he saw Saint Peter and he was human.
Jesus claims that he has no powers as a mortal, yet in the episode Sleigh Ride Down, he uses supernatural powers to heal Santa's broken legs.
When the rabbits are surrounding Stan, there are two rabbits in a car. Look at them when they are in the car and after they get out. They are completely different. Not only do they change from being fully masked to having their faces showing, but one of them changes colors from white to brown.
In this episode, Jesus asks Kyle to kill him. The ironic thing about this is that in Passion of the Jew, Kyle and his Jews are blamed by Cartman for killing Jesus. Now, Kyle knows now that a Jew really did kill Jesus: himself.
Second appearence of Pope Benedict XVI.
Everyone at The Hare Club For Men wears full Easter Bunny Costumes, but Randy just wears ears, a nose, and buck teeth. Stan, in the final sequence, is dressed the same as his dad, with only ears, nose and buck teeth.
Stan being surrounded by the Easter bunnies is very similar to when he, Kyle and Kenny were surrounded by the Ginger Kids in the episode Ginger Kids.
Bill: Jesus, we thought you died.. in Iraq.
The last time Jesus appeared on the show was during the episode Red Sleigh Down, in which he was shot and killed by an Iraqi gunman.
Bill: Take them into custody!
Stan: Hey, what the hell?!
Pope Benedict XVI: Bill, we have the rabbit. It's all we need.
Bill: Don't be soft, Your Holiness! These "whores" must be punished in front of everyone!
Kyle: You swore on the cross, fatso!
Bill: Yeah. Too bad for you... it was a double cross! Hahahahahahaha!
Randy: Oh, we should've seen that coming!
Pope Benedict XVI: Bill, I'm not sure that double-crossing people is very Christian.
Bill: IT IS WHAT CHRIST WOULD'VE WANTED!
Jesus: Who are you to say that?!
Randy: Oh thank God! Hand it over, Stan! They're gonna kill me! Give them the rabbit!
Pope Benedict XVI: Yes, hand it over.
Stan: First, you have to promise you won't hurt it! And that you'll let everybody go!
Pope Benedict XVI: We promise.
Bill: We swear it on the cross!
Randy: JUST HAND OVER THE BUNNY, STAN!
Stan: Okay, fine. (A cardinal takes the rabbit, Randy is released)
Randy: Stanley, why did you do that? I would have proudly died for that rabbit.
Stan: You said "hand over the bunny!"
Randy: No! That is NOT the way we're remembering it!
(Randy & Stan in the car on the way to The Hare Club meeting)
Stan: Dad do I have to wear this bag over my head the entire time?
Randy: You aren't a member yet. You can't know where our secret meetings take place. Where going to a distant location, an old building near a lake about 40 mins away.
Stan: You mean the old Galverson lodge?
(there's a short pause then Randy takes the bag off)
Randy: I wanted to keep this from you Stan. I really wanted to wait till you were older, but... you just had to keep asking questions.
Stan: Why were those other rabbit guys chasing me?
Randy: We have to be careful when we think that somebody is on to us. We are all part of a secret society Stan. A very accient, very important society of men who follow the way of the rabbit, that protect the secret of the easter bunny. We are called The Hare Club For Men.
Stan: Does mom know about this?
Randy: Dah, it's The Hare Club For Men, chicks wouldn't understand.
Stan: I don't understand.
Randy: I belong to a secret society that has been around for thousands of years. Our identities have to be protected.
Stan: Could you take off the ears, please?
(Timer on microwave counting down)
Ninja 1: What's that?
(look of recognitition and absolute horror)
Ninja 2: PEEEEEEPS!!!
(Stan and Randy enter the Lodge)
Hare: Stan Marsh - Welcome, you must be very excited!
Stan: Must I?
Grand Hare: All hail the cute rabbit Snowball!
Hares: Hail Snowball.
Stan: Jesus! You did answer my prayer.
Jesus: Actually, I was answering the prayer of Nick Donovan.
Nick Donovan: Oh that's me, Neat-O.
(Jesus and Kyle are locked in a separate prison cell apart from Pope Benedict XVI's cell; Jesus furiously saws at a chain keeping the door closed with a file in his right hand)
Pope: (in remorse) Forgive me, Jesus.
Jesus: (furious about Bill Donohue) We'll never get out in time to stop him!
Kyle: Don't you have any superpowers?
Jesus: (throws the file away) Not as a mortal. Only in death. (pauses for a second, then realizes) Wait. That's it. We have no choice, Kyle. You're going to have to kill me.
Kyle: (shocked) What??
Jesus: Stab me with this. (brings out a small dagger) If I die, I can resurrect outside the bars.
Kyle: (reluctant) N-no way! Do it yourself!
Jesus: Suicide is blasphemy. There's no choice here, Kyle!
Kyle: Dude, you don't understand, I'm a Jew. I have a few hangups about killing Jesus.
Jesus: Just make it quick. (kneels down and hands the dagger to Kyle, then points at his own neck) Through the neck. I'll arise again immediately.
Kyle: (looks at the dagger in dismay) Don't make me do this.
Jesus: My son, there is no time! DO IT!
Kyle: (still looking and pondering) Eric Cartman can never know about this.
Jesus: (still kneeling, looking at Kyle) I understand. And Kyle... Happy Easter. (waits patiently for his moment of death and rebirth)
Kyle: (pauses, then reluctantly) Happy Easter, Jesus.
(He stabs Jesus in the throat, and at once Jesus stands up in pain with a gargling scream, his blood spewing everywhere from his throat; still screaming, he walks around for a few seconds while smearing blood on the wall, his choked screams and groans turning silent, then falls forward to the floor and dies; his halo falls from his head and rolls away with a metallic clink)
Kyle: (in shock at seeing Jesus' body) ...Jesus?
Randy: Stanley I'm so proud of you. You've learned so very much this Easter.
Stan: Yeah, I learned not to ask questions, just dye the eggs and keep my mouth shut.
Randy: That's my boy.
Stan: (Praying) Jesus, I know we haven't talked in a long time. And I know that every time you appear we end up killing you somehow, but... I don't know what to do and I could really use your help.
(Long pause while Stan looks up and around expectantly for some sign his prayer has been answered)
Kyle: I think the rabbit just crapped on my jacket.
Bill: Take him to be tortured!
Pope: Tortured? But Bill all this torturing and ninjas, it just doesn't seem very Christian.
Bill: You asked for the help of the American Catholic League... Let us do our job! Take him!
Randy: NO! NO You bunny hating bastards, don't do this!
Stan: Look, I'm just saying that somewhere between Jesus dying on the cross, and a giant bunny hiding eggs there seems to be a gap of information.
Kyle: What happened?
Stan: (quickly) My dad's in a rabbit worshiping cult called The Hare Club for Men, they protect the secret of Easter, but before they said what it was they were attacked by ninjas and put me in charge of snowball.
Kyle: I'm kind of finger painting right now.
Professor Teabag: Look at the Pope's hat. It makes no sense. Except that is was originally designed for a rabbit.
Bill Donohue: This Easter, I'm going to start by making our rabbit stew ten times meatier!
Bill: Kill Him!
Bill: He goes against the church, he must die.
Pope: Alright, that does it Bill. I'm pretty sure killing Jesus is not very Christian
Bill: You are soft, weak. You leave me no choice. Take them.
(Ninja's handcuff Jesus and the Pope)
Marvin: There's my grandson. I'm real proud of you Billy!
Cartman: And I want a Baltor Soldier doll for Easter, and 5 Crash'n' Go RC cars, you got that? DO YOU HAVE THAT!?
Man in Easter Bunny Suit: Uh, don't you think that's-
Cartman: N-No! You don't ask me questions. You are a rabbit, I am a human, so if you don't bring me what I want for Easter, I can ****ing kill you!
(Snaps Picture, Cartman leaves)
Cartman: Bye, Easter bunny!
Stan: You don't see the missteps in logic with that? Look, I'm just saying that somewhere between Jesus dying on the Cross and a giant bunny hiding eggs there seems to be a a gap of information.
Randy: Stanley, just dye your goddamn egg!
Stan: I don't feel like coloring eggs! I don't get it! (leaves)
Randy: What is wrong with him?!
Sharon: Well, he's just getting older, Randy. Maybe he figured out the Easter bunny isn't real.
Randy: (slams his fists on the table) You know so little!
Stan: Uh, can I ask a question? Why do we do this.
Randy: Wh.. What do you mean why do this? It's Easter.
Stan: Right, so why do we color eggs?
Randy: So... So the Easter bunny can hide them.
Stan: Yeah, but why?
Randy: Stanley, Easter celebrates the day that Jesus was resurrected after being crucified for our sins.
Stan: So we dip eggs in color vinegar and a giant rabbit hides them?
Randy: That's right.
Pope Benedict XVI: Where is the rabbit?
Randy: I don't know... and even if I did know, well, I'd probably tell you because I don't want to be here anymore.
When Stan says "They found me" as the ninjas come, Stan sounds like Cartman.
This is the first Easter Special. But it is actually the second episode to take place during Easter. The first being Quintuplets 2000.
The sacred bunny's name is Snowball.
Kenny doesn't appear in this episode.
Mortal Kombat: When Jesus throws the bladed throwing star at the false pope, he does a stance move that Kung Lao from the hugely popular game Mortal Kombat as Kung Lao throws his bladed hat in a simular fashion.
Randy: ...in my Easter Bonnet, with all the frills upon it, I'll be the grandest lady in the Easter parade.
While coloring Easter eggs, Randy is singing the Irving Berlin song "Easter Parade," made famous by the 1948 musical by the same name. The musical won the 1948 Academy Award for Best Scoring of a Musical Picture.
When Stan is running from all the Easter Bunnies and is at the bathroom door to get his dad to open up, it is similar to the film Teen Wolf when his dad opens the door and he too is a werewolf.
When Stan and Randy are at T.H.C.F.M. One of the SUV's rearbumper reads "Thummer" which is a spoof for Hummer
When the ninja attacks the professors house, he puts peeps in a microwave, sets the time, and waits.
This is based on a scene from the movie Under Siege where Steven Seagal uses the microwave as a bomb.
The scene where Jesus asks Kyle to kill him so that he can be brought back to life is reminiscent of recent plots of Battlestar Galactica, in which Cylons ask to be killed so that they can be resurrected in another body in order to escape from prison, get board enemy ships, have visions, etc. The music played during this scene is simlar to that of Galactica as well.
The Road Warrior:
When Stan's dad is talking to him in his room Stan has a poster in his room called The Street Warrior, this is a joke on Mel Gibson's Mad Max Movie The Road Warrior.
Jesus cuts Bill in half with the star, catches it, then puts on the shades. This is a reference from a scene in Blade II.
The blade that Jesus kills him with is the same blade from the 1983 movie Krull.
Hair Club for Men:
The phrase Hare Club For Men is a play on the phrase Hair Club for Men; a business which originally specialized in toupees and hair pieces for bald men, then later incorporated hair transplant treatments.
The Easter chant done by the Hare Club for Men. Sounds like it is just a straight translation of the first part of Here Comes Peter Cottontail.
Here comes Peter Cottontail
Hoppin' down the bunny trail,
Easter's on its way
The brand name of Professor Teabag's TV is 'CONY.' This is a spoof of SONY, a Japanese multinational corporation and one of the leading manufacturers of electronics.
This spoof is also relevant to the plot because "coney" is another term for rabbit.
Bill Donohue is the leader of the Catholic League. Has been known for his criticism of South Park. Particularly with the episodes "Bloody Mary" and with the end of "Cartoon Wars (2)," and this is his first appearance in an episode of South Park.
The Da Vinci Code:
The episode is a farce to the book and movie, The Da Vinci Code. In the episode, it contains the "Hare Club For Men" which is like the Priory of Sion. The club was created to protect the ancient secret of Easter.
Also, instead of Professor Teabing in TDVC, there is a Professor Teabag.