I've been trying to find the name of this old cartoon for a long time now. From what I remember there is a pirate ship (made of wood and sialed via sails) that traverses space. In the particular scene in my mind they are in some sort of asteroid field and I believe there are fungus like growth inside the cave of one of the larger asteroids. I don't remember much else about it but I'm pretty sure it's a movie.

You could start your search here;

List of space pirates - Wikipedia, the free encyclopedia (http://en.wikipedia.org/wiki/List_of_Space_Pirates)

Hope that helps a little?

Not much info given, but, it could be Walt Disney's Treasure Planet.

Was it a ship sailed by people called Bob?

I was thinking Treasure Planet too