- Anti-Climax Boss: Wily Machine 1, which is suprisingly easy compared to the level you had to go through.
- Breather Boss: Cut Man and Bomb Man. Cut Man's attacks are sluggish and easily dodged, and Bomb Man is more likely to kill you through Collision Damage than he is with his bombs.
- Demonic Spiders: Big Eyes will be the bane of many players' existence. Three hits from one kill you, they have two jump patterns (and only one can let players get past it) and they take 20 buster shots to kill. So of course they put one at the end of the stages of 2/3 of the game's Robot Master roster AND put three in a row at the beginning of Wily Stage 1.
- Ensemble Darkhorse: Guts Man is often considered the most iconic Robot Master from this game, if not the entire series. Not surprisingly, many people were pissed that he didn't make it into Dr. Wily's Revenge for the Game Boy (and, by extension, any of the Game Boy games).
- Good Bad Bugs: The famous "Pause Trick" glitch, which allows you to rapidly pause the game while an attack like the Elec Beam is passing through an enemy, allowing them to take multiple bits of damage from the same shot. This is often used by gamers to beat Yellow Devil. In fact according to some, it's the only way to beat him.
- Ladders are the most borked in this game (and Capcom could never quite get it right), making it possible to clip through walls and move faster than the graphics can load.
- Harsher in Hindsight: "Fight, Mega Man! FOR EVERLASTING PEACE!" This line becomes sad when you put into consideration what happens in Mega Man X and especially Mega Man Zero. To put it this way: Mega Man never attained everlasting peace.
- Polished Port: The Wily Wars rerelease.
- Suspiciously Similar Song: Elec Man's theme is either this to Journey's "Faithfully" or REM's obscure song "All the Right Friends".
- The stage select theme also sounds like the beginning to BonJovi's "Runaway".
- Tearjerker: A retroactive example, see Harsher in Hindsight above.
- That One Boss:
- Elec Man, whose weapon is powerful enough to kill you in three hits from full health! God help you if you fight him without the Rolling Cutter.
- Fire Man, if you don't know the trick to beating him. He is extremely aggressive, and his shots drop trailing fire right over your position as you jump over them, and the time they stay vary. If you don't know said trick, your only other hope is coming in with enough health and using Ice Slasher.
- Ice Man can also kill you in three hits, and will likely do so if you didn't bring Thunder Beam with you and you aren't used to the timing of jumping through his attack pattern.
- The Yellow Devil, a boss so tough that the Pause Trick, a trick where you pause when he's taking damage, is considered a totally genuine/guilt-free strategy for beating him.
- That One Level:
- Guts Man's stage and those damn moving platforms which keep rotating 90 degrees.
- Ice Man's stage, if you're doing it without the Magnet Beam. There's a large chasm you must cross on Foot Holders, moving platforms that drift back and forth at seemingly random intervals. In addition, they fire at you while this is going on and it's perfectly possible to fall right through one upon a seemingly-successful landing. And then about halfway across, penguins will start to Zerg Rush you. Without the Magnet Beam, it really starts to feel like a Luck-Based Mission.
- Wily Stage 4. You have to fight Bomb Man, Fire Man, Ice Man and Guts Man all in a row and if you die, you have to restart from Bomb Man all over with no chance to refill your ammo. Not only that, but there's no health pickups along the way either.
- The beginning of Wily Stage 1, where you have to fight through three Big Eyes.