For full clarification:
Popo is Male, has always been
Kaiba/protagonist is Male, switched genders when in Chroniko's body, but he's back to male.
Neiro is Female, switched to male once, back to female now.
Hyo hyo is a thingy
The Space Ostrich is a badass and has no need of genders
Warp/King-Douchebag-the-Third is male
Whatsher/hisface who conspired with Popo to depose Dada is ambiguous