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As far as Schengen is concerned, you are planning two trips. The first is to Austria, the second is to the Netherlands and Germany. You could do that with two separate single-entry visa. Multiple-entry visa are usually granted for the convenience of the visitor and the visa officials after several problem-free single entries.
- Since your first trip is to Austria, you definitely have to apply for an Austrian Schengen visa.
- The time would be tight to apply for the second visa after the first trip, so you could mention both in the same application and hope for the best. If they grant you a visa with enough entries and duration/validity, you can use it on the subsequent trips.
- If not, for the second visa the "main destination" rule mentioned by Henning in his comment applies. You count days if there is no specific reason to go to one of the countries (e.g. a business meeting in the Netherlands, followed by some sightseeing in Germany).