Continuity Nod: The title itself is a reference to Going Commando.
Even Maximillian's office in the Series 60 release looks more like half of a normal hallway instead of a room.
Bizarrchitecture: Despite taking place within a Secret Agent Clank Vid-Comic, all of the levels with the exception of the Maktar Casino don't resemble anything spy or supervillain related, being more themed around circuitry.
Cliffhanger: Ratchet and Clank have collected every piece of the MCGuFIN, not knowing where it will send them.
Baleful Polymorph: The Boar-Zooka weapon, which turns all enemies except the Security Tanks and final boss into boars.
However, the Series 40 version only has it once in the entire game whereas the Series 60 version has several instances.
Backtracking: Both versions require you to return to previous levels after acquiring the Circuit Jammer in order to destroy special blocks.
Action Bomb: The Explodo enemies, which detonate when close to Ratchet.