Badass Moustache: Grows a thick, American police chief-worthy manly moustache in Rearmed 2.
Empowered Badass Normal: In addition to his arm, Spencer has a number of secondary bionic improvements that, for example, provide armor, weaponize his adrenaline, allow him to jump superhuman heights and fall hundreds of feet without injury, and more. He looks mostly human, but he is far from it.
One-Man Army: In the NES version, he's the sole representative of the "FF" Double Force, wielding a Bionic Arm as a unique grapple wire. Expanded storylines explain this as him being an experimental soldier supplied by the TASC bionics division.
Averted somewhat in Chain of Command and Rearmed 2; TASC has a period where their bionic technology is in great demand following the Imperial Incident, leading to Spencer training the next generation of bionic commandos as a Major.
Officially, when Nathan Spencer originally lost his arm, he was the first person to be considered and tested on for bionic augmentation. He was therefore the most important part of the Research And Development department for bionics. When he went into the field, he was humorously given the codename Rad from all his time in the labs.
Super Drowning Skills: Spencer's bionic arm is extremely heavy, and almost completely shuts down when exposed to water. Spencer therefore cannot swim in water as his arm drags him down.
You Don't Look Like You: The original design, Rearmed, Chain of Command and Rearmed 2 all at least seem like different stages of the same character - his Game Boy and 2009 / Marvel vs. Capcom 3 appearances look entirely different without any explanation whatsoever.
Sudden Sequel Heel Syndrome: Besides his major role in the original Bionic Commando, Joe was the player character in at least three other Capcom games back In the 1980's and 1990's. He then became the Big Bad of the 2009 game.
Composite Character: The Rearmed version of this character combines the original role of the nameless helicopter pilot and a minor (but important) soldier (which the Game Boy version instead combines with Super Joe).
Gender Flip / Name Change: The NES character was a male soldier named Hal, which was changed to a female pilot named Haley in the Rearmed remake.
Moral Myopia: Considers civilians to be legitimate targets and their mass murder an act of "self-defense" because of the government's (admittedly pretty evil) treatment of Bionics in the Purge. She never reconsiders this, and only helps Spencer and turns against the BioReign leader Super Joe at the end because she felt he was just using her and the other Bionics as pawns.