As of Paint it White England is officialy a secret agent/wizard/pirate/ninja
Ghost in the Shell brings us the Major: a ninja cyborg bisexual police-officer assassin hacker VR porn star.
The Demonic Tournament in Yu Yu Hakusho includes, amongst other things, humans with spirit/psychic powers, demons reincarnated as humans, an ancient-turned-young midget martial arts master, demon shapeshifters, demon ninjas, human zombie cyborgs, a demonic artist that can kill you by painting you and a demon drunken master.
For extra super bonus points, the Macross 7 OVA Dynamite 7 has the rock band with guitar-controlled Transforming Mecha fight interstellar poachers to Save TheSpace Whales.
Mazinger Z: The Iron Masks and the Iron Crosses are corpses the Big Bad reconstructed using cybernetic parts and reanimated, programming them to serve him faithfully. Hence, the are cyborg zombies. Besides, the Iron Masks wear uniforms resemble the armor of an ancient Greek soldier, and the Iron Cross's uniforms remind of Nazi soldiers. It is fitting since his leader IS an ex-Nazi officer turned cyborg by the Big Bad.
Volfogg in GaoGaiGar. Come on, he's a giant RobotNinja spy that transforms into a Police car. And can combine with a transforming Motorcycle and Helicopter on top of THAT.
Compare his Zonderian rival for the first parts of the anime, Pinchernone (or Penchinon, if you prefer it), who compromises the Pirate Zombie Robot of the trope title. In human form, he takes the form of a sailor, and he is always seen sitting and with a huge grin on his face. Late in the series, back as Tomoro-117, he actually befriends Volfogg, with Volfogg commenting on him as an "interesting friend".
Before Volfogg, there was Dagshadow from Brave Command Dagwon who can transform into a robot, dragon, and jet.
And before Dagshadow, there was Shadowmaru from Brave Police J-Decker who can transform into six different forms!
In GaoGaiGar FINAL, they certainly showed just how badass Volfogg is. While getting his ass kicked, he managed to get away, set up a holographic projector, hide, and backstab Polturn... WITHOUT POLTURN NOTICING! Must be because of his Seiyuu, The Great Kamina.
The pirate Perry from the manga Burning Hell. He is a pirate who uses a high speed fighting style based on Voldo-like claws. On chains. Also, he is dead and keeps on moving thanks to his captain's dark magic. He doesn't have any robotic parts but making this trope 3/4 literal still deserves some credit.
The whole point of Kujibiki Unbalance was to make a show with every possible anime trope to give the characters in Genshiken something to talk about. Witches, aliens, ninjas, whatever, for a mere three episodes.
Come on down to Cromartie High School, and you'll get to meet the likes of delinquents, robots, aliens, monkeys, and some dude who looks like Freddie Mercury from Queen. Those are all students, by the way.
Robots? What robots? I haven't noticed any robots around Cromartie. I hope you're not considering Mechazawa to be a robot, just because he has very shiny, pale skin! He's just as normal as the rest of us!
Soul Eater has a blue zombie ninja teaching in the school sponsored by the Grim Reaper. His weapon partner is a brown-skinned mummy nurse!
Is it a blue zombie ninja, or is it a blue zombie with ranger/sf/random-elite-military training. Or is it a blue zombie ninja with ranger training?
We forgot to mention that the Big Bad's army is made up of cyborg zombies. Cyborg zombies with giant robots.
Cyborg zombies with giant robot zombies which come from another Giant Robot that can merge with a Space Colony and zombify other giant robots.
The Gundam Maxter is a boxing surfing cowboy football player. Oh, yes.
The original Mobile Suit Gundam has some instances of this also, most obviously in episode 37 (or 36 for English-speakers), "The Duel at Texas." Samurai vs. Knight in the Wild West IN SPACE!!
The Witchblade anime indeed features some ninja zombie robots... more precisely, saboteur/assassin zombiewerecyborgs and combat robot zombies. Latter just because they were deemed more expendable than human soldiers with comparable equipment.
Neon Genesis Evangelion brings us giant Artificial Humans inhabited by the souls of the dead, wearing armor as a Restraining Bolt, and turned into cyborgs so they can be controlled by human teenagers that hook their nervous system directly into them.
A ridiculous amount of things in Getter Robo, particularly anything created by the Dinosaur Empire (since all their creations are by default "Dinosaur + 'x'". A T-Rex attached to a twin-barrelled giant tank being backed up by dinosaurs with guns riding on the backs of dinosaurs with missile pods attached while robot pterodactyls fly overhead? Happens all the time[1]◊.
The reason why the Jeremiah/Sayoko pairing in Code Geass is so popular. He's a cyborg and she's a Ninja Maid.
Biomega, or to be more specific, Kozlov Grebnev. I mean, cyberpunk and zombies are cool, cyberpunk zombies are even cooler but a Russian talking bear with a sniper rifle is in a league of his own.
Kisame from Naruto: he's a shark-man that uses a shark-tooth sword that he can ride like a surfboard, will come back to him if he drops it, and cuts into the hands of anyone else who uses it.
Let's not forget about Sasori, who is a ninja Brain in a Jar inside a puppet with built-in flamethrowers, water cannons, rotor blades attached to a pole on his back, and a poison-covered cable/tentacle in place of his stomache. And that puppet is inside another puppet with built-in poison Whip Sword.
Can't forget Zetsu. He's a cannibal venus fly trap man whose face halves argue with each other and can teleport from place to place by phasing into the environment. And he can split those halves apart.
One of Pain's bodies appears to be a some of kind of ninja cyborg. In fact all of Pain's bodies could be considered ninja zombies depending on how you look at it.
Kidomaru of the Sound Four is a ninja spider-man gamer who can use a giant bow and arrow.
Shippuuden's first filler arc has the Leaf Village under attack by zombie ninjas. They even drool.
And has an ass-chin. Let's not forget Big Bad's ass-chin. Fay's eyepatch is more Eye Scream than Eye Patch Of Power, given that he lost said eye when said half-chinese Kid Hero's clone ripped it out and ate it.
The 2010 Ironman Anime Adaptation preview by Madhouse: TonyStark flies around futuristic Tokyo to battle the White-Haired Pretty Boy villain's army of humanoid mecha fired from a missile launcher. The villain himself has Beehive Barrier and a Powered Armor that looks like medieval armour.
Quite possibly the most disturbing example of this trope: cyborg zombie fish.
Kujako-Oh the Peacock King. Buddhist ki-and-bead shooting monks ala Donovan vs nazi-summoning demons, demon-summoning nazis, demonic nazis, cybernetic demonic nazis with Gatling arms, and a bishounen vampire nazi robot who isn't even aware he's a robot. And it's done in an incredibly serious and dramatic fashion. Yes, really. There's absolutely no comedic value behind any of it as opposed to some of the lunacy in Fullmetal Alchemist. And at one point the nazis went to war with one of the demon lords. And won! Also, FMA appears to have a shoutout to one of the movies, King Bradley looks a heck of a lot like the demonic nazi gaufuhrer, who plays a similar role to the anime's Dante. (He's the BVNR's subordinate, until the BVNR's robot form is revealed when he's supposedly killed, at which point he reveals his eyepatch hides not the mark of the homonculi, but is home to the Final Boss of the demon army!) HSQ drinking games with this series will leave one a soused and broken wreck.
Hazuki from Moon Phase is, to quote Professor Otaku, a lolicon vampire catgirl ballet surfer. How cool is that?
Outlaw Star has Magic Ninja Space Pirate Ship Robots.
Bleach is about magic ghost samurai. With an added bonus of magic ghost samurai ninjas in the Second Division, the Eleventh is the Magic Ghost Samurai Hot Blooded Hooligan Division, and the magic ghost samurai Mad Scientists in the Twelfth.
By the most recent arc, you have five species; Human, Soul Reaper, Vizard, Arrancar, and Fullbringer. Ichigo's been four of those, and is usually a Human/Reaper.
Between the beginning and end of any series connected to Bubblegum Crisis, the Boomers will evolve from standard cyborgs into magical floating fusing ghost zombie cyborgs.
The villains of DinoZaurs are dragondinosaurvampiric skeletal alien Transformers (okay, those are aliens too, but these aren't made of metal) with glowing eyes. The heroes are the same, except for the fact that they're not dragons, not vampiric and not alien, and thus considerably less awesome.
And the main character had a fully-earned Fan Nickname of Chinese Electric Batman.
Ranma ½ has Pantyhose Taro, who has a cursed form made up of a Yeti, bull, eel, and chicken, with an octopus later added to the mix, and was named by an evil perverted old man.
Apparently, the new villain is an ordinary high school girl who is actually a Magical Girl Zombie Ninja Vampire... Serial Killer.
In Sailor Moon all the Sailor Scouts are not only magical warriors, but also alien princesses (from their respective planets). Rei, a.k.a. Sailor Mars, is also an Alien Princess Magical Warrior Temple Priestess, and Hotaru, a.k.a. Sailor Saturn, is a Psychic Alien Princess Magical Warrior.
At the end of the first season, almost all of the Sailor Scouts are killed off, only to come back as apparitions for the final battle, making them Alien Princess Magical Warrior Ghosts.
A more fitting represenative for this trope, one of the Negaverse monsters from the first season sent to spy on the Sailor Scouts is an Alien Ninja Paparazzi.
Brigadoon: Marin and Melan has the Gun-swordsmen: three robots who sport swords on one arm and guns on the other. In addition to having Healing Factor, they can also fly.
The protagonist of Vassalord is a devoutly Christian cyborg vampire who works for the Vatican. And he wears glasses.
You forgot his Dual Wielding, cyborg former best friend who wears a giant teddybear head with a respirator in it.
And the Giant Monk with a rocket launcher in his backpack. Another monk is a cyborg that talks like a stereotypical black preacher with ho's and has a Red Right Hand.
Ladies, gentlemen and critters, observe a screenshot◊ from Full Metal Panic, where you may see an elf with taser gun and a teddy bear running around in body armor.
In Azumanga Daioh, the girls are having problems deciding which theme they should pick for the School Festival. Overused ideas like a café, or a haunted house are quickly dismissed. Then they start talking about combining those (and with cute things as a third idea), then Osaka gives us this gem:
