Common ''secret'' commands,
Most people know these commands and are pretty common.
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1.) Undead Horse- /summon EntityHorse ~ ~ ~ {Tame:1,Type:3}

2.) Skeleton Horse- /summon EntityHorse ~ ~ ~ {Tame:1,Type:4}

3.) Huge Wither Boss- /summon WitherBoss ~ ~ ~ {Invul:10000,CustomName:Dinnerbone}

4.) Giant- /summon Giant~5 ~ ~

5.) EnderCrystal- /summon EnderCrystal ~ ~ ~

Here are some unique ones,
Many people don't known these at all.
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1.) Power X sword- /give @p diamond_sword 1 0 {ench:[{id:16,lvl:10}]}

2.) God Sword- /give @p diamond_sword 1 0 {ench:[{id:16,lvl: 10000}]}

3.) Rideable Enderdragon- /summon Minecart ~ ~1 ~ {Riding:{id:"EnderDragon"}} (Show that Dragon who's boss! >:D )

4.) Snow Golem riding Iron Golem- /summon IronGolem ~ ~ ~ {Riding:{id:"SnowGolem"}}

5.) Over Powered Skeleton riding Skeleton Horse- /summon Skeleton ~ ~1 ~ {Riding:{id:"EntityHorse",Type:4,Tame:1,SaddleItem:{id:329}},Equipment:[{id:261,tag:{ench:{id:50,lvl:1},{id:48,lvl:5},{id:49,lvl:2}]}},{id:313},{id:312},{id:311},{id:310}]}

6.) Summon Killer Rabbit- /summon Rabbit ~ ~1 ~

7.) Ride the Ender Dragon in a boat- /summon Boat ~ ~ ~ {Invulnerable:1,Riding:{id:"EnderDragon"}}

8.) Flying animal stack- /summon Chicken ~ ~5 ~ {Riding:{id:"Ozelot",Riding:{id:"Wolf",Riding:{id:"Pig",Riding:{id:"Sheep",Riding:{id:"Cow",Riding:{id:"EntityHorse",Tame:1,Riding:{id:"Bat"}}}}}}}}

9.) Chicken Jockey- /summon Zombie ~ ~1 ~ {IsBaby:1,Riding:{id:"Chicken"}}

[10.) Flying pig- /summon Pig ~0 ~0 ~0 {Riding: {id: "Bat"}}/size]

11.) Skeleton riding skeleton horse- /summon Skeleton ~ ~ ~ {Riding:{id:"EntityHorse",Type:4,Tame:1}}

12.) Mob Stack- /summon Zombie ~ ~1 ~ {Riding:{id:Slime, Riding:{id:MushroomCow, Riding:{id:Creeper, Riding:{id:Villager, Riding:{id:Skeleton, Riding:{id:Spider, Riding:{id:Chicken, Riding:{id:Pig, Riding:{id:Cow, Riding:{id:Sheep, Riding:{id:PigZombie, Riding:{id:Enderman,Riding:{id:CaveSpider, Riding:{id:SnowMan, Riding:{id:Witch}}}}}}}}}}}}}}}}

13.) Charged Creeper- /summon Creeper ~ ~ ~ {powered:1,ExplosionRadius:100}

14.) The Ghast that shots TNT- /summon MinecartSpawner ~ ~1 ~ {Invulnerable:1,EntityId:PrimedTnt,SpawnData
{Motion
[0.0,0.0,1.0],Fuse:60},SpawnCount:3,SpawnRange:5,RequiredPlayerRange:30,Delay:100,MinSpawnDelay:100,MaxSpawnDelay:100,MaxNearbyEntities:5,Riding:{id:"Ghast",Invulnerable:1,Rotation:[270f,0f],NoAI:1,Riding:{id:"Giant",Equipment:[{id:tnt,Count:1},{},{},{},{}],Invulnerable:1,Rotation:[270f,0f],NoAI:1}}}

15.) Stacked Slimes- /summon Slime ~ ~ ~ {Size:0,Riding:{id:"Slime",Size:1,Riding:{id:"Slime",Size:2}}}

16.) Rideable Wither- /summon Minecart ~ ~1 ~ {Riding:{id:"WitherBoss"}}

17.) Summon Elder Guardian- /summon Guardian ~ ~ ~ {Elder:1}

18.) Invisible cow- /summon Cow ~0 ~0 ~0 {Invulnerable:1}[/size]

19.) Skeleton Rabbit- /summon Skeleton ~ ~1 ~ {CustomName:"Dinnerbone",Riding:{id:"Skeleton",Equipment:[{id:391}]}}

20.) Generic Vilager with green cloak- /summon Villager ~ ~ ~ {Profession: 5}

21.) Your own head- /give [your username] minecraft:skull 1 3 {SkullOwner:"[username]"}

22.) Spider pig- /summon Pig ~0 ~0 ~0 {Riding: {id: "Spider"}}

23.) Horse carrying chests- /summon EntityHorse ~0 ~1 ~0 {Attributes:[{Name:generic.maxHealth,Base:53.00},{Name:generic.knockbackResistance,Base:0},{Name:generic.movementSpeed,Base:0.22},{Name:generic.followRange,Base:16.00},{Name:horse.jumpStrength,Base:0.70}],Motion:[0,-0.08,0],Health:43,HealF:42.50,ChestedHorse:1,Items:[],OwnerUUID:,Variant:0,Rotation:[-293.45,0]}

24.) World edge- /tp 29999999 80 29999999[/size]

25.) Slime Tornado- /summon Slime ~ ~1 ~ {Size:7,Riding:{id:"Slime",Size:6,Riding:{id:"Slime",Size:5,Riding:{id:"Slime",Size:4,Riding:{id:"Slime",Size:3,Riding:{id:"Slime",Size:2,Riding:{id:"Slime",Size:1}}}}}}}