Here's the list of episodes in the order in which they were produced. This is how the official site lists them, and also how they are ordered on the DVD sets.
Season 1[]
Episode 1: The Deep End
Episode 2: Junk in the Trunk
Episode 3: Nightmare Generator
Episode 4: The Sack
Episode 5: Nutcracker Sweet
Episode 6: Gold Dust Gasoline
Episode 7: Kiddie Pool
Episode 8: Plastic Buffet
Episode 9: A Piece of the Action
Episode 10: Toyz in the Hood
Episode 11: Vegetable Funfest
Episode 12: S&M Present
Episode 13: Badunkadunk
Episode 14: Toy Meets Girl
Episode 15: Midnight Snack
Episode 16: Atta Toy
Episode 17: Joint Point
Episode 18: Operation Rich in Spirit
Episode 19: That Hurts Me
Episode 20: The Black Cherry
Season 2[]
Episode 21: Suck It
Episode 22: Easter Basket
Episode 23: 1987
Episode 24: Celebrity Rocket
Episode 25: Federated Resources
Episode 26: Dragon Nuts
Episode 27: Cracked China
Episode 28: Rodiggiti
Episode 29: Password: Swordfish
Episode 30: Massage Chair
Episode 31: Metal Militia
Episode 32: Veggies for Sloth
Episode 33: Sausage Fest
Episode 34: Drippy Pony
Episode 35: The Munnery
Episode 36: Adoption's an Option
Episode 37: A Day at the Circus
Episode 38: Lust for Puppets
Episode 39: Anne Marie's Pride
Episode 40: Book of Corrine
Season 3[]
Episode 41: Werewolf vs. Unicorn
Episode 42: Tubba-Bubba's Now Hubba-Hubba
Episode 43: Squaw Bury Shortcake
Episode 44: Rabbits on a Roller Coaster
Episode 45: Tapping a Hero
Episode 46: Shoe
Episode 47: Endless Breadsticks
Episode 48: Yancy the Yo-Yo Boy
Episode 49: More Blood, More Chocolate
Episode 50: Robot Chicken's Half-Assed Christmas Special
Episode 51: Celebutard Mountain
Episode 52: Moesha Poppins
Episode 53: Ban on the Fun
Episode 54: Losin' the Wobble
Episode 55: Slaughterhouse on the Prairie
Episode 56: Boo Cocky
Episode 57: Bionic Cow
Episode 58: Monstourage
Episode 59: President Evil
Episode 60: Chirlaxx
Season 4[]
Episode 61: Help Me
Episode 62: I'm Trapped
Episode 63: In a DVD Factory
Episode 64: They Took My Thumbs
Episode 65: Two Weeks Without Food
Episode 66: Tell My Mom
Episode 67: I Love Her
Episode 68: But Not In That Way
Episode 69: Love, Maurice
Episode 70: P.S. Yes, In That Way
Episode 71: Dear Consumer
Episode 72: We Are a Humble Factory
Episode 73: Maurice Was Caught
Episode 74: Unionizing Our Labor
Episode 75: President Hu Forbids It
Episode 76: Due to Constraints of Time and Budget
Episode 77: The Ramblings of Maurice
Episode 78: Cannot Be Erased, So Sorry
Episode 79: Please Do Not Notify Our Contractors
Episode 80: Especially the Animal Keith Crofford!
Season 5[]
Episode 81: Saving Private Gigli
Episode 82: Terms of Endaredevil
Episode 83: Big Trouble in Little Clerks 2
Episode 84: Kramer vs. Showgirls
Episode 85: Malcolm X: Fully Loaded
Episode 86: Robot Chicken's DP Christmas Special
Episode 87: Major League of Extraordinary Gentlemen
Episode 88: Schindler's Bucket List
Episode 89: No Country For Old Dogs
Episode 90: Catch Me If You Kangaroo Jack
Episode 91: Beastmaster & Commander
Episode 92: Casablankman
Episode 93: The Departy Monster
Episode 94: Some Like It Hitman
Episode 95: The Core, The Thief, His Wife and Her Lover
Episode 96: Casablankman II
Episode 97: The Curious Case of the Box
Episode 98: The Godfather of the Bride II
Episode 99: Fool's Goldfinger
Episode 100: Fight Club Paradise
Specials[]
Episode 1: Robot Chicken: Star Wars
Episode 2: Robot Chicken Christmas Special
Episode 3: Robot Chicken: Star Wars Episode II
Episode 4: Robot Chicken: Star Wars Episode III
Episode 5: Robot Chicken DC Comics Special
Episode 6: Born Again Virgin Christmas Special
Episode 7: Robot Chicken DC Comics Special 3: Magical Friendship