I am attending two independent conferences in Germany that are one month apart. Ideally, I want to apply for them concurrently, with minimal costs. I will fill two applications, and book one interview. Beyond that, do I have to pay the fees twice? Can I apply for a single multiple entries visa for a duration that covers the two conferences instead?
If you submit two visa applications, then you'll be paying for both of them. The fees are for processing each individual petition.
I would say that this is a situation that justifies applying for a multiple entry visa, but ultimately that is up to the visa officer. If you have a previous travel history which is good, then you shouldn't have a problem securing a multi-entry visa to cover both conferences.