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Not that I'm changing my decision, I just want to help out anyone who dares defend Megaman. Samus would win but heres a list of not even close to all of Megamans weapons.

Thunder Beam-The user fires three streams of lightning up, down, and forward. This attack is capable of destroying barriers.

Metal Blade-Immense saw blades made of "Cermicaltitan" are thrown by the user. They can be thrown in eight main directions, and are quite powerful. However, the user is immoblilized while using them on the ground.

Pharaoh Shot (MM4) / Pharaoh Wave (MM2:TPF)-(Pharaoh Shot) Working by acc**ulating solar energy, the Pharaoh Shot is chargable like the Atomic Fire weapon, resulting in more damage. It fires a large ball, followed by a subsequent charged particle shot. The Shot is can be fired in six directions. The charged Pharaoh Shot is formed above the user and is offensive when using it to contact enemies.
(Pharaoh Wave) This weapon fires two waves of heat energy in front of and behind the user.

Gravity Hold-This weapon dispels the current areas effect of gravity, and allows the user to launch enemies into the air by unleashing a gravitational force up to 20 G, immediately followed by a minus pull (upward/reversed/anti-gravity).
This one might not work on Samus though.

Power Stone-The user creates a whirling stone attack where three stones spiral away from his/her location in clockwise direction. It is very inaccurate, however. In Power Fighters, it unleashes a stone hand that races along the ground.

Centaur Flash (MM6)/ Centaur Arrow-(Centaur Flash) Releases a flash of energy that goes across the whole screen while distorting time-and-space.

(Centaur Arrow) The user fires illuminated arrows randomly that project as a slightly diagonal upwards or downwards angle.

Knight Crush-Fires at a maximum of two mace balls that return to the user after travelling a short distance. It can be shot in diagonal directions.

Junk Shield-Similar to the Leaf Shield, except utilized with pieces of debris surrounding the user. Three green magnetic cores are set up with 120 degrees evenly separated as concyclic points which attract junk debris. The shield can be kept as a defensive barrier or fired away by the user as a weapon.

Thunder Bolt-The user fires of a large bolt of electricity that can stun foes upon impact. It splits into 2 smaller balls and can charge up certain electrical devices.

Slash Claw-A short range melee weapon in which the user surrounds his or her fist with energy to damage the foe. In Mega Man: The Power Battle, the Slash Claw is chargable.

Noise Crush = Crush Noise-Fires off a sound wave that disorients enemies. An added use is that the user can absorb a wave if the Crush is reflected from a wall, and then the user can release a larger shot.

Flame Sword-The user slashes a flaming sword, lighting up flammable objects. If on the ground, the user is immoblized while using the weapon.

Homing Sniper-A small homing missile is fired. When charged, a total of six targets are available. The allocation, however, seems to be random.

Flash Bomb-A large concussion grenade can be shot. Upon impacting an enemy or onto walls, a group of offensive light spheres glows for a while, lighting up the area.