Here is the complete list of museums in Amsterdam that give free access with the Museumkaart. All important museums are included (This includes Anne Frank House, Rijksmuseum, Van Gogh Museum, Stedelijk Museum).
There are some 8 or so museums in Amsterdam that DO NOT give Museumkaart access; it is safe to say that all of these are smaller, less important museums (yes, to some extent this is a matter of taste).
Museumkaart