What mode of travel are you using between Amsterdam and Munich? If by car, beware of the drop fees!

Travelforbeer (love the name) thanks for that advice. Do you have any idea on the fees? like an approximation?

Consider stopping by the Rhine Gorge - the best part of The Rhine, between Rudesheim and Koblenz and take K-D boats along the river, hop off to trek up to castles or to visit a winery.
www.k-d.com for boat schedules.
Check these sites for lots of info on the Rhine boats - www.seat61.com; www.ricksteves.com and www.budgeteuropetravel.com.

And yes check car drop-off fees - you may want to take the train from Holland to say Cologne and pick up your car and also visit the world-famous Gothic Cologne cathedral right next to the Cologne trains station. See www.bahn.de - the German Railways web site for schedules and fares, including deep discounted ones if you book far in advance.

trip suggestions between The Netherlands and Munich are appreciated>

Great stops pretty much on the main route:

Cologne (for the cathedral)
The Mosel Valley - Cochem makes a very sweet place to stay and everyone raves about it - on one of the prettiest river valleys in Europe - the Mosel Valley and close to the Rhine Gorge so you can base there - if no car then trains and boats will get you everywhere
Heidelerg - one of the few cities in Germany not suffering major war damage in WW2

From Heidelberg drive down the Castle Road - a river valley studded with old towns and castles - to Rothenburg - one of the nicest walled towns in Europe

Then take the Romantic Road via Dinkelsbuhl and Nordlingen - two gems of old towns - to Munich.

chb-

I just checked a major car rental company on-line and it looks like the drop fee for renting a mid-size car with stick shift in Amsterdam and dropping in Munich is $400-$500 for a 2 week rental in May2013. You can check other car rentals on -line to compare rates, drop fees, etc.

PalenQ provided very good advice for the rest of your trip.

I did a trip similar to yours several years ago with the exception of throwing in a few days in Paris. I took the train from Amsterdam to Paris then to Frankfurt. I picked up the car in Frankfurt, toured the Mosel and Rothenberg, then on to Munich where I returned the car. The in-country drop fee was about $20.

If you do rent a car, be sure to return it as soon as it is feasible when you hit Munich. The public transportation there is very good. Depending on your hotel, you may have to pay a hefty parking fee ($25-$30 per day)if you keep the car. And I hope you already have hotel reservations for that time in Munich...

Forget my last comment, I see you alreay have an apartment rented in Munich. The car return comment is still valid ...