Fondue is a method of cooking in which food is dipped in cheese, chocolate, or oil. The process involves a dipping sauce wherein you coat your food with the help of a skewer with the sauce before eating it. Popularly two types of sauces are used - Cheese and chocolate. Cheese fondue is usually accompanied with foods like breads, crackers, crudites etc...whereas chocolate - anything that goes well with chocolate like strawberries, cookies etc. The criteria for the dipping sauce should be the consistency which should perfect for dipping and coating.
Ganache on the other hand is a cream and chocolate mixture mostly used to make frosting or filling. The texture can vary from light to thick depending on the recipe...light for a simple coating or for drizzling to a dense consistency to make something like say Truffles. Making ganache is extremely simple - Bring some heavy cream to a boil, add chunks of chocolate to it until it starts melting. This is called chocolate cream. Add butter to it to make it glossy.