Wild Fury lets me destroy ships belonging to my opponent - their choice. I played this last night and my opponent wanted to chose ships which had been captured by Wild Fungus. We decided he couldn't, but I felt uneasy about this ruling as it really hosed that player (he had to chose between losing his power or a foreign colony) and we couldn't find anything explicit in the rules.

Any thoughts on this?

Just off the top of my head, without my game nearby...

If you mean that your opponent wanted to ships of his which had been captured by the Wild Fungus flare, then no, he can't. They're not his ships anymore; they're a subset of the stack belonging to his opponent.

Kobold Curry Chef said:

Right ... you can't voluntarily do anything with your ships that have been captured.