In order to survive a disease, Bunnie D'Coolette (Archie's Sonic the Hedgehog) must have her robotic limbs upgraded with a cooler design.
Frank West (Dead Rising/Dead Rising 2) can make some weapons to kill enemies more efficently
Chuck Greene (Dead Rising 2) can invent some deadly weapons so he could kill his enemies more easily
But neither Frank nor Chuck had made some crazy weapons as Nick Ramos (Dead Rising 3). His mechanical skills can turn even the most harmless toys into deadly weapons.
Edward Elric (Fullmetal Alchemist) had his automail limbs upgrade to survive cold temperatures, be more durable, and faster against foes (manga/Brotherhood).
Buccaneer (Fullmetal Alchemist) gets new automail limbs put in...
...for a cooler and stronger design
The Tessaiga (InuYasha) is capable of absorbing demonic energy and powers from an opponent in order to obtain new and powerful abilities.
Jak's Morph Gun (Jak and Daxter series) is capable of being outfitted with numerous upgrades that allow it to possess several eco mods with weapons for each, as well as increased ammo capacity, damage output, and rate of fire.
Mario & Luigi (Mario & Luigi: Superstar Saga) had their hammers reforged to break harder rocks.
Stark used an Asgardian metal, Uru to repair Captain America's (Marvel) shield and made it stronger than ever
Whenever his regular formula for his web-fluid is not enough, Spider-Man (Marvel) can create different versions of his formula for dealing with the situation such as a type that can resist fire.
Moon Knight (Marvel) upgraded his trademark weapon, the Truncheron, to adamantium with a cable hook
X (Mega Man X series) is able to enhance his abilities and weapons via various armor pieces he finds throughout his fights in the Maverick Wars.
For example, X's First Armor allows him to dash on the ground and in their air, increase his resistance to damage, and fire a more powerful Charge Shot.
X's Fourth Armor increase the power of his body and weaponry, and also grants him the Nova Strike ability.
In his Ultimate Armor, X possesses all of the enhancements provided by the Fourth Armor with much greater power, and can use the Nova Strike for an unlimited amont of time.
Mega Man X's (Marvel vs. Capcom: Infinite) X-Buster was upgraded by Iron Man into the Infinity Buster, a massive cannon powered by the Infinity Stones, in order to destroy Ultron-Sigma.
Kankuro (Naruto series) added a few weapons to Sasori's body before adding it to his puppet collection
The Dragon Sword (Ninja Gaiden) is capable of being upgraded as well being infused with the Eye of the Dragon.
Franky (One Piece) used Vegapunk's military technology to vastly upgrade all the artillery installed in his bionic body.
Many Rangers (Power Rangers/Super Sentai franchise) are able to use enhancement modes such as the Lights of Orion (Lights of Ginga in Japan) to upgrade their weapons.
Rachet (Rachet and Clank series) is able to use the Nanomites he gathers from defeated enemies in order to upgrade the strength of his weapons.
Haru (Rave Master) had the Ten Commandments reforged by Musica when it was broken to make it more durable. Also it changes shapes when different powers were used.
Kazuma (s-CRY-ed) was able to gain more power for his Shell Bullet after making contact with the Crystal Alter.
E-102 Gamma's (Sonic the Hedgehog) upgrades include a laser blaster to lock onto more enemies and a jet booster for hovering.
The Ancient Light (Sonic Adventure series) allows the characters to posses various power-ups for certain levels.
Nightmare (Soul Calibur) wields Soul Edge which was a normal sword before bathing it in the blood of countless victims. Because of this it becomes stronger when it comes in contact with blood.It can also restore its strength with every shard of Soul Edge found.
Spyke (Splatoon) can increase the amount of sub-ability slots a piece of gear has in exchange for gold or Super Sea Snails (sitting next to him in this picture).
The Master Sword (The Legend of Zelda series) is Link's most trusted weapon. Even in its final form, its power can be increased by smithing or magical means...
...in some cases, resulting in the Tempered Sword, and the Golden Sword, doubling and eventually quadrupling its power.
The Sword of Omens (ThunderCats) repels Mumm-Ra when the Eye of Thundera was inserted into it
Lion-O (ThunderCats 2011) used the Spirit Stone to power up his gauntlet and added a laser beam to it.