As of Paint it White England is officially 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 YuYu 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.
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.
The design of the titular mecha also counts. Many described the Mazinger as a Demonic Knight Fortress, and in case of Mazinkaiser Demonic Knight Fortress Body Builder wearing a diaper.
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.
Speaking of Katsuyuki Konishi, his role in Dennou Boukenki Web Diver is Garyun, who is basically a Pirate Ship Zombie Robot Electric Swordsman Dragon in Cyberspace. Yeah its as absurd as it sounds.
Basically the whole series is made on this trope. All the Web Knights, for example are a combination beetwen a Verhicle and an Animal or mythological creatures.
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.
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?
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◊.
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 and is capable of firing a Rocket Punch full of poison needles.
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.
The 2010 Iron Man anime adaptation preview by Madhouse: TonyStark flies around futuristic Tokyo to battle the 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.
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.
Bleach There are four main soul groups: human, hollow, shinigami and quincy. Within these groups, there are 'tainted' forms as represented by Vizards (hollowfied shinigami), Arrancar ("shinigamified" hollows), and fullbringers (magical humans born to hollow-tainted human parents): Ichigo is the most bizarre mixture of any character in the manga. His father is a shinigami who underwent "humanification" to make him a shinigami/human hybrid. His Quincy mother was hollowfied by a hollowfied shinigami; Ichigo's inherited humanity and shinigami from his father, and humanity, hollowfication, quincy and shinigami off his mother. He's human, hollow, shinigami and quincy all rolled into one.
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.
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 Senshi 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 Senshi 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 Dark Kingdom monsters from the first season sent to spy on the Sailor Senshi is an Alien Ninja Paparazzi.
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:
Vinland Saga: The protagonist, Thorfinn, is a Viking boy who fights with dual daggers and is often sent on scouting and assassination missions. Oh, and he's a member of what is essentially a pirate crew. Viking Ninja Pirate?