Attack Its Weak Point: Almost every boss has these little circular bubbles for weak points. You quickly get used to spotting and destroying them. If you can't see any, shoot its head. Only a very few bosses subvert this pattern, and those are all about your size. The Annihilator has a second. If you can't hit the head because it's facing away from you, shoot for the tail!
Attack Reflector: The Blade. Apart from cutting through dirt and metal, it allows you to reflect some of the enemies' shots. The reflected shots don't hit the enemies, but the Blade itself inflicts damage.
Bittersweet Ending: The threat of Cruiser Tetron is ended forever, but Flip Hero is dead as well.
Doubly so since the question of whether Cruiser Tetron created Flip Hero to try and kill himself for good or Flip Hero went rogue is never answered directly. If it's the former, then the ending is bittersweet for both Flip Hero and Tetron!
The Reaper Drone takes this to its logical extreme.
The Grand Mother is this on multiple levels — it spawns Mothers, which are themselves Mook Makers. The Guardian also has statues at the top of his room that come to life after you damage him enough, and the Liquid Metal Processor is a more standard example. Seems like Daniel really likes this trope.
Plasma Hydra is a variation of this. Blow off one head, out pops the next! Fortunately, at most 3 heads in a row pop up (in Normal mode, that is). So, not quite sequential boss, but a case of sequential boss targets.
Hard mode has elements of this. You can do this as well to a limited extent if you find the Expel ability. Just make sure to keep an eye on your health.
Though the Plasma Hydra boss fight has shades of this, it becomes ridiculous in Hard mode.
Annihilation's final boss fight.
Canon Welding: Annihilation mode will seem familiar to fans of Daniel Remar's other big game.
Subverted; the fact that Annihilation takes place on the Ciretakolooks like it's supposed to make Hero Core canon to Iji, but in his official guide, Daniel states that Annihilation mode isn't canon and he just did it to get people wondering about it.
I Cannot Self-Terminate: Cruiser Tetron is eternally locked in the cycle of dying at the hands of Flip Hero and being rebuilt and trying to destroy earth again. Killing him is the only way to end this, though it's questionable whether or not Tetron himself is a big fan of dying.
Intentional Engrish for Funny: One of the game's three language settings is "Retro!", and when selected it will display all messages and dialog in humorously-broken English.
Luck-Based Mission: The behavior and fire patterns of several enemies is random. For instance, fighting the Guardian or an Annihilator-with-mook on hard mode is a lot easier if you get lucky with their movement.
Mercy Kill: The final fight against Cruiser Tetron is implied to be one of these, as you free him from the endless cycle of hate that he's locked in. It's really driven home by the final form, where Tetron is unable to even stand, limited to lying prone in the corner and feebly trying to hold up his arm to shoot you.
Metroidvania: It's a blend of this and Shoot 'em Up. Also a slightly unusual example, as none of the upgrades are required to reach the final boss, though getting there without the item received for killing your first boss requires using a secret move.
Minimalist Run: See Metroidvania above. Furthermore, a Bonus Boss is only accessible on one of these. Annihilation mode is also this. You don't get any upgrades from bosses, and it's much more linear.
Mistaken for Granite: Guardian's room contains some statues of standard enemy machines you fought many times. Appearing to be decoration, they actually are idle machines and aid the boss once he loses a certain amount of Hit Points.
Spawners, which were the only Mook Makers in the original Hero.
Mothers are archetypal for this; however, other foes note Hunters create Spews, Warp Eidolons create Phazes. The first boss casually creates some Drones. have this habit, even if they only create Mooks as a side effect of, for example, firing their Wave Motion Gun. One boss even spawns Mothers, making it a Flunky Boss on multiple levels.
Tetron is this in the back story.
Multiple Endings: There are at least two endings to the game. Beating the game with all computers used gets you the best ending.
Nintendo Hard: Normal mode is fairly easy, but Hard is brutal. Annihilation is worse.
Rank Inflation: In the boss rush, there are five ranks above A: "Hero", "Lord of Game", "You can stop now", "Seriously", and "reallyjoel's dad". The last few aren't intended to be achievable, but Daniel Remar put them in based on the ridiculous performance of certain Sacred Grounds runs.
Recurring Boss: You have to destroy several Generators to progress, just like in the first. Also, the Eliminator/Hunter-Killer, who attacks many times until you are powerful enough to beat him.
Sequence Breaking: You can bypass most of the game and get to the final boss with Expelling.
Marathon Boss: Fittingly, the Plasma Hydra in Hard Mode. Also, Tetron and the Guardian.
Series Mascot: Flip Hero seems to be this for Remar Games, seeing as he gets referenced in a few other games that have nothing to do with him and appears in the Remar Games logo in the Garden Gnome Carnage Flash version. In a strange variant of the trope, he's not even from Remar's most popular game.
Useless Useful Spell: Both the Expel ability and the Blade are pretty much useless in combat. However, both have a specific function in speedrunning, and the Blade can slaughter certain enemies and bosses. Also, Shapeshift is mostly for fun
Wall Master: The Eversion-like hands suddenly coming out of walls in Hero Forever. They don't damage you, but "just" steal your flags (that's bad already, though, since collecting flags is the point of Hero Forever) and will really creep you out the first time you encounter them.
One of them even takes you to an easter egg in Annihilation mode.