A couple of suggestions (no idea how hard these would be to animate):
- crushing the penis or balls, either by someone holding two stones or with a special machine
- destroying the penis with crocodile shears (which are probably fictional, but it's a cool idea):
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- placing the penis on a wooden block and cutting it off with an executioner's axe
- putting the penis (still attached to the owner) into a meat grinder
- putting the penis on fire while it's still attached
- melting the genitals with acid
Additionally, IMHO it would be great if we could see more of the existing castrations and penectomies from the victim's POV.