This is a VERY fun Map, and with the amount of barriers for Zombies to come in through, finding all these smaller Easter Eggs are difficult to find and locate, or you may end up missing them entirely.
Here's some small things I've found, and feel free to add to this!
- FREE MINIGUN + TIME BOOST + CUPCAKES
You read that right as Rainbow Dash! YOU can get a FREE Minigun as well as a time extension for the Minigun Power Up!
To do this is REALLY simple.
STEP 1: Open up the Power door
Head to the Meat Storage Room where The Mystery Box lies.
To the Right of the Box (When you're facing it) You're going to see a bright Red light, open the door and turn on the Power.
-This one is probably the most frustrating just trying to get there.. but fret not! Make use of the Mystery Box (Say Hi to The Muffin Mare, Derpy, who's chilling in the corpse box.. and probably made into Muffins herself) and make use of that to fight off the Zombies pouring in.

STEP 2: Activate the Console!
To the Left of the Power Switch, There's a console. Make sure you press it and you'll hear a small 'Boop'. That's how you know the console has registered your input. it will go from saying "SEND SIGNAL" to "SIGNAL SENT"

STEP 3: Find the SECOND Console
Now that the button has been pressed, run down the Stamin-Up hallway till you get to the intersection with Mule Kick. Clear the Boxes and head UP the Stairway, then take a left. There's a small gated doorway that you'll need to buy. BUY IT! Once it's opened up, the Console will be on the Left. There will be a Prompt that says "Receive Signal". Press it, and you'll have 'Signal Recieved' along with a confirmation boop.

STEP 4: Find the THIRD and LAST Console
TO THE RIGHT! Go through the opening on the Right of the passage way you opened, and enter the console room that leads to Pinkie Pie's OTHER torture chamber.
The console is on the Right of the room. Press it, hear the boop, and You're all set.
-If you're trying to do the Main Easter Egg, Twilight is up the stairs you pass up.

STEP 5: Rinse and Repeat
Now Here's where I still get confused from time to time.
This WHOLE thing is something you have to REPEAT at least 3 times.
Run back to the Power Room, Press the button, and run back and check the consoles, pressing them each time. By the last time, You'll be given 3 confirmation Boops.
CONGRATS! You've now earned yourself a Minigun that lasts nearly the whole round! Not only that, every time you pick up a Minigun Power Up, it will now last for a whole 45 SECONDS!
..So What about the Cupcakes?
Well, That's the song you get to listen to while you're mowing down Zombies in a nice 8-Bit tune!
OTHER SECRETS

1.) SECRET SONG!!- Shadow Moses by Bring Me The Horizon
- FIND THE CLEAVERS!
There are 3 of them. There's no specific order.
-The First one is in one of Pinkie's Kitchen/Dissection rooms. This can be accessed by going through the LEFT doorway (Same side as the Barrier) and go to the last room on the Right. The Cleaver is on the Counter. Press your interact Key and you're set.
-The Second one is located ALL the way down in Pinkie's LARGE Torture Chamber (The One with Trixie's head mounted on the wall). Make your way to the table directly across from Trixie's head and you'll see a piece of meat with a Cleaver in it. Interact with the cleaver and it's time to move on!
-The THIRD AND LAST Cleaver is in THE MAIN TELEPORTER ROOM. Do not confuse this for the Power Room. This is super easy to find. It's literally to the LEFT of Double Tap.
Enjoy your song :)
NOTE: THIS EASTER EGG IS REPEATABLE!!! Enjoy the song as many times as you like!

2.)The GHOST of the GREAT AND POWERFUL TRIXIE!
-Find Trixie's head mounted to the wall and interact with it. You'll be greated with a voice line from Trixie.. and Trixie is still as boastful as ever, even in death.
This is one of the Unlisted Secrets KraZy was talking about.

3.) SHOOTABLE EASTER EGG!
-Behind nearly every barrier are several bright screens. Make sure you shoot them, and you'll see a bright Purple flash of light as well as the 'interact' sound you hear when you mess with an Easter Egg thing. Make sure you look EVERYWHERE around the inside of the barriers so you don't accidentally miss one.
-The Minigun or getting the Infinite Ammo Power UP (Plus an automatic) is the best for this because you can shoot in there as much as you want and possibly hit something you may have missed.
-When I say look everywhere.. I do mean EVERYWHERE. Behind the corners of the barriers and above the Teleporter.. Even Pinkie's Prize room (Accessible via the Main Easter Egg). The hardest one to locate is to the LEFT of Jug. Hidden behind a filing cabinet is the shootable screen. The best way to hit is by using an explosive weapon.
If you shoot them all, you're rewarded with a Perkaholic!

4.) JUMPSCARE EASTER EGG
-When you reach the Pack-A-Punch Center, Shoot The Pack-A-Punch.
Usually this is what triggers it, otherwise just look around the sky. It won't always trigger due to a bug.
*EDIT!!!* Zeus, in the comments, has identified that the trigger is by shooting the top window of Sugar Cube Corner. I've done it a few times, so it's 100% confirmed. It's also repeatable! Thanks for the help, Zeus!

5.) Free points!
-Prone Under the Perk Machines, get a free 100 Points for each machine

6.) The Cell Wall Buys
-Use the Teleporter. There's a small chance that you'll be temporarily transported into a cell with one of the wall buys (Stakeout and the HAMR- Both obtainable in the Box) or Widow's Wine. In the comments, Zeus explains everything available in the Cells!

7.) BUILD THE SHIELD!!
-You can find parts of the Zombie Shield scattered about the Map.
1 is located Next to Stamin-Up
1 is located in the Power Room
1 is located near the Large Torture Room
Alternatively,1 may also appear in the MP5K room, the Central Control Room, next to the book shelf along the piles of trash (Near Mule Kick), inside of the Deadshot Daiquiri room, or the Kitchen/Dissection room.

8.) BUILD THE PARTY CANNON!!!
-It's time to party with this buildable!
1 part is in the empty room with the MP5K just along the doorway.
1 Part is in the Cells blocks
1 Part spawns IN one of the Cells (Which you can get to by using the teleporter)
Alternatively, the parts will spawn in the Control Room (Under the shelf in the corner), in the Meat Locker, or the Storage Room (With Electric Cherry)
NOTE 1: I built Pinkie's Party Cannon around Round 30, so the Cannon was really only making crawlers around that time. Just a forewarning that it is NOT a "Save Me" Wonder Weapon.
NOTE 2: You CAN Pack-A-Punch the Party Cannon, and it becomes "Pinkamina's Hell Fury Party Canon Devastator!" (More info in section 11)

9.) Russian Nesting Doll EE
*EDIT* : So i followed the Hint from Zeus (In the comments of this guide) and managed to locate Rainbow Dashes Nesting doll. After determining the code, I found the Easter Egg!

-Found a weird Pink Nesting Doll back in the Large Torture Chamber. Shot it and it disappeared. Apparently, these are representations of the Characters, and the Pink Nesting Doll represents Pinkie Pie. It is the only one that disappears after hitting it.
It is located on a shelf near the Bathroom. Look on the Right when facing outward and you'll see it.
-Rarity's is literally right around the corner, next to the burning area. It's white, and the Cutie Mark is hidden by the Shadows, and requires a closer inspection. Shooting it does nothing.
-Fluttershy's is in the Electric Cherry Room. After turning on power, make your way to the cells, buy both doors, and look to the RIGHT and at the ground. You'll find Fluttershy's Nesting Doll chilling next to a suitcase. Shooting it does nothing.
-Rainbow's is located inside of a trash can next to Speed-cola

If you manage to get the order correct (Pinkie Pie, Rainbow Dash, Fluttershy, Rarity, in that order), You will be rewarded with a free Nesting Doll Tactical Equip!


10.) Right next to the Speed-Cola Machine is a Full Map of Equestria! This is from "The Elements Of Harmony" Official Guide Book!

11.) Pack-a-Punch MLP Custom names + Secrets (Meaning all the Special Names):
NOTE: Yes, You can Double Pack the Guns on this Map, in case you were wondering. Dead Wire and Thunder Wall will probably be your life saver.
-The RPD will become "Applejack's Punishment Device" with 300 Rounds in the Clip and 1000 in the reserves.
-The DINGO will become "Luna's Genocide"
-The AUG will become "Twilight's Vengeance" with 90 in the Clip and 630 in Reserve. (Discovered by User MClovin in the Comments)
-The M60 Machine Gun will become "Fluttershy's Roar". It has 240 In the Mag, and 950 In Reserve.
-Pinkie Pie's Party Canon (The buildable Wonder Weapon) will become "Pinkamina's Hell Fury Party Canon Devastator!" IT HAS NO SPLASH DAMAGE AND A WIDE RANGE. Go nuts with it. It has 25 in the Clip, and 75 in Reserve. It can also be Double Packed, so have fun killing literally everything in your path.
-The RPK will become "The Resonating Heart of Fire 115" (A reference, of course, to Black Ops Zombies)
-The HAMR will become THOR's HAMR (Funny, huh?)
-The KSG will become the KOMRAD SACRIFICIAL GALANTLY. (It sucks... Like Communism. Always buy American.)
-The Python will become Rarity's Sapphire & Bloodstone. (Thanks to Zeus for hinting out the custom name!) and it's a pretty powerful duel weapon.
-The Raygun Mark II will become Porter's Destiny.

12.) The Jar
-Yes, the meme lives on Here while the Ponies around you do Not. After using the Teleporter, you may randomly end up in the HAMR Wall Buy cell. Look to Your RIGHT and you'll see a Small Jar chilling on top of a Heater with Rainbow Dash chilling inside. She looks like she's waiting for a shower.. or something.

13.) SPECIAL COSTUMES!
-I have no idea how these are triggered, I noticed that when I was Pack-A-Punching a Gun, Rainbow Dash had Her Wonderbolts Costume on. (War with King Sombra, Variant)
*Edit * Zeus has gone on to state that the Costumes are triggered by unlocking the portal. This is true, and each pony will wear a variant of the Season 5 War with Sombra battle armor.

14.) FREE FIRE SALE!
(Found another one of Your Hidden secrets, Zeus!) In the Meat Locker, just outside of the Power Room and next to the Mystery Box is the Corpse of Derpy. RIP the Muffin Mare... or so you think!
Walk up to the deceased corpse, press and hold the interact button for about 10 seconds. Eventually, You'll hear a scream from the corpse and Pinkie's evil laugh.
You will then be given a Fire Sale... And wouldn't You guess what You have sitting right next to You! This is REALLY helpful in the early game to get better guns before "Brutus" show up.

15.) Twilight's Radio calls
(After 2 years lol)
After activating the power, there are what sounds to be an emergency call over a radio in several areas around the map. Shooting around the areas shuts off the audio playing.
1 is around Double Tap
1 is by Speed Cola
1 is by Mule Kick
1 is around the upstairs terminal (From the torture chamber...I think. I could have just heard it from Speed-Cola).
I utilized the party canon to shoot around the area and hit all 4(?), walked around the Map and couldn't hear any more broadcasts. There may be an interact item somewhere, I just haven't found it... Or it could just shut them off.

BONUS:
-Pinkie Pie (The Player) has full voice acted custom lines and will change what Twilight says when interacting with Her. (And She's pretty good.)
-Round 38 is a Special Round. Brutus Ponies will continuously Spawn until you've killed them all. Ending the Round will NOT stop the Brutus Ponies from spawning.

As of current- This is everything that I have been able to find. Feel free to add to this if you can find anything else that either I may have missed, or completed something that I haven't!
Good luck Everypony!