I'm from Somalia and living in South Africa; I have a refugee travel document issued by South Africa. Can I get a Schengen visa to travel to Germany or The Netherlands with it? Do the German/Netherlands consulates issue visas to such a document holder?
Refugee travel documents issued by South Africa are (according to lists maintained by the European Commission) recognized by most Schengen countries except Estonia, Latvia, Malta and Poland. So you should be okay for Germany and the Netherlands.
Remember that you still need to apply for a visa in your travel document.