In theory twice:

• Once when you enter the Schengen zone where you'll have to declare items in your carry-on. Otherwise you might - when joining all the intra-Schengen passengers - hand it to someone flying within Schengen who will not have to declare it at the destination.
• Once when you actually arrive. You'll have to declare anything in your checked luggage (that can be identified by the missing green stripes on the tag)

In practice, transit customs when entering Schengen are rare. Usually there's a desk just behind the immigration officer with a couple of customs agents or nobody at all and just a bell to ring someone.

In the past, I usually made the declaration at my destination as it prevents me from having to discuss twice with customs agents.