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When fighting a boss, you can score multiple hits with the same shot by pausing the game after the first "hit". After the boss has stopped flashing, quickly hit select to unpause the game and then again to pause it again. You will score an additional hit. Keep hitting select until the boss is defeated. You can beat many bosses with one shot this way. This does NOT work with the standard arm cannon.
A less notable, but still occasionally useful, consequence of this is that when you press Select when Mega Man is hit, it will reduce the brief "knockback" period.
If you are using a controller with a Turbo capability (or an emulator that does the same) and activate the Super Arm weapon, sometimes you can pick up and throw blocks without the block actually disappearing. This comes in handy when fighting the boss at the end of the third leg of Dr. Wily's Castle.
There is a point in the Iceman stage where you try to get a 1-up but often miss it. When you drop down to the next screen (the one before the Big Eye), use your magnet beam and try to climb your way up and try to hop onto the off-screen platform where the 1-up is supposed to be. The moment you step on it, the screen will glitch and show you falling to the screen below and avoiding the Big Eye in the process.
While this requires very precise timing, you can teleport through monsters.
When you pause or unpause the game, Mega Man enters his warp animation but retains his vertical velocity. This can allow jumping through or falling through enemies as necessary, but only works in some situations.
The magnet beam allows you to create a platform at any location. Its implementation has a few exploitable bugs.
If a magnet beam is placed at a precise location below a ceiling (within 1 pixel, Mega Man will be propelled to the right.
If you reach the top of the screen (such as with the magnet beam) when the area is open, you gain access to the bottom of the screen. As such, you can zip across sections that have a lower floor, or jump through the top of the screen to travel downward.
As with zipping, placement of the magnet beam has to be precise.
Magnet Beams cannot be fired through walls, unless you grow it in one direction, and switch the direction of the beam while it is growing.