The PAL version of Shinobi X/Legions has some pretty awesome new music composed by Richard Jacques, who also did the music for the Saturn port of Sonic 3D Blast. This version is considered by many to be superior since it sticks truer to Koshiro's style. Compare the original version of stage 1 to Jacques' version.
Breather Boss: Lobster is this in Master System Shinobi. Squeezed in-between the infamous Mandara and the brutal four-phase long final boss against the Masked Ninja is by far the easiest boss in the game, who does nothing but slowly walk towards you and raise his sword up and down. When his sword is raised up he blocks your attacks, but all you really have to do is get one hit in and you've already won as he's also vulnerable immediately after being knocked back, making it laughably easy to take him out in seconds. Lobster could also be considered a breather in between the Platform Hell that was just before his fight and the hectic Masked Ninja stages immediately after.
Game-Breaker: The Art of Mijin. The explosion, while costing you a life, also restores your health meter, takes out nearby enemies, and deals a crapton of damage to bosses. More importantly, it respawns you in place instead of at the last checkpoint, preventing you from losing a large amount of progress. It also gives you another use of your special moves, so you could just use it over and over. (Until your lives run out, at least.)
Goddamn Bats: Many of the "minienemies" that appears in the PS2 game have shades of this. Also, in earlier games, the ninja who were airborne had a rather nasty ability to wreck your jumps with very well placed shuriken.
Good Bad Bugs: In the Master System version of Shinobi, the Mongol at the beginning of level 3-1 on the second floor can be killed with your nun-chaku— by striking the left side of the screen.
Hilarious in Hindsight: One of the Terminator/Hulk boss' attacks is charging forward with a crescent-like energy covering him. That would look a lot like Hulk's Gamma Charge attack.
Shinobi is a synonym for a "ninja" (specifically of its first kanji) and not the name of a particular character.
Both the Ninja Master and the Shadow Master are frequently called "Neo Zeed," which is the name of the criminal organization they are in charge of.
Iron Woobie: Hotsuma in the PS2 game has it pretty rough. At the beginning of the story, he forced to take the role of the Oboro clan leader and Akujiki's new wielder after killing his brother, Moritsune. As the story progresses, his clan members have been killed and brought back to life as Hellspawn for him to kill and feed Akujiki. By the end of the game, his only option to seal away Akujiki is by killing Hiruko with it before allowing himself to die as the Golden Palace collapses.
Misattributed Song: Despite having worked on the soundtracks of previous entries, Yuzo Koshiro did not compose for Shinobi III. While that game's soundtrack lacks the experimental flair of Koshiro's work, it's awesome enough in its own right that the mistake is easy to make.
The Game Over screen from The Revenge of Shinobi can be startling at first, due to the Big Bad laughing out of nowhere, and somehow, laughing just once makes the Game Over screen much more haunting than when he spammed his Evil Laugh during the time you actually fight him.
That One Boss: In the PS2 ''Shinobi'', chances are it's Hiruko. Using "TATE" attack is essential to killing him because your normal attacks barely scratch him. You have a very short window to attack him because you can't hurt him when he attacks and he teleports around the arena and any missed "TATE" combos when hitting him are lost with no chances for anything other than normal hits. On top of this the only enemies you can get a "TATE" on are these talismans he that don't have features to differentiated the front or back from making it hard to tell which side you should even attack to set up the "TATE", and they fire projectiles at you which can interrupt it, and when he summons large numbers of them you can get pummeled with projectiles on top of Hiruko teleporting in close to attack you with his fans. Most of his attacks aren't very hard to dodge if you are focused on him, if you are trying to build up a combo you can easily get hit from attack coming from off-screen.
What an Idiot!: Ageha is quite a sore loser. Ok, her love interest Moritsune was killed by Hotsuma in a duel in order to keep Akujiki sealed, but then she suddenly decides to resurrect him...by freeing the archenemy of the Oboro clan who eventually proceed to kill everyone, turn Moritsune into a living puppet and eventually disposing of her.