Spend the maximum amount of time in Berlin. It's a beautiful city with a ton of fantastic museums (assuming you like museums). Find your way to the Potsdamer Platz, it's pretty cool to walk around there, and it has a movie theater with movies in English, which is cool if you're looking to relax and sit for a couple of hours.
Munich is pretty nice, though I haven't spent much time there (I've only been twice even though I've lived in Germany for most of the last 9 years, and once was only for a few hours when I did a college interview with an alumni who worked there). Leipzig I've never been to.
Amsterdam is a great city, and I'd also recommend visiting The Hague. I've spent quite a bit of time there, and it's a thoroughly charming city, with some cool things to see, and some very nice restaurants. If you do go there, find your way to the beach, it's beautiful, in a gray, cold, storm-tossed kinda way (though it might be significantly nicer in the summer, I've only ever been there in January). Also, there's a hotel called the Kurhaus you should find. I mention this not because you should stay there (not that you shouldn't, it's quite nice, I just hesitate to offer accommodations advice) but because near that hotel you can find a very nice little mall/shopping type area nearby if you need something, as well as an Italian restaurant that serves dynamite Calamari. Down on the beach nearby is The Pancake House, which serves a large, thick crepe filled with your choice of toppings (I recommend the apple, butter and bacon for a nice lunch/dinner pancake, but there are tons of others for both entrees and desserts). That place is awesome.
As a final note, awesome choices on countries. I've found Germany to be amazing to live in, and I really enjoy Berlin. The Netherlands is also very nice. The weather can sometimes leave something to be desired, but speaking generally, Germany and The Netherlands possess beautiful, well-maintained, relatively clean cities and countryside, which makes them awesome from the start. Public transportation is very available, and I hope you're planning to make use of the rail system, because it's really quite excellent.
Edit: Munich is the capital of Bavaria, Ascension, and is also the home of Oktoberfest, which ironically enough begins in September and ends very early in October. So you can get shots of him loaded and in lederhosen.