One cutscene where Ms. 'Splosion Man reveals herself in a disguise brings to mind Total Recall, down to the disguise's head laughing before it explodes.
And before the Bionic Bommando boss fight, she arrives in a Johnnycab from the same movie.
Ms. Splosion Man: What the heck are you? Mighty Eternal: Wh-wh-wh-what the heck are you? (The Boss then initiates a very familiar self-destruct sequence.)
Not to mention that in the middle of the sequence, the boss says "Heeeeere's Johnny!"
One of Ms. Splosion Man's idle dances is the Carlton.
Several of her idle animations contain notable parts from the music video of All The Single Ladies
Her other idle movements include jumping in victory like Chun Li and doing the Macarana.
During the final boss battle (which in itself is a shout out to Punch-Out!!), Ms. Splosion Man says: