What do you want to see? You've got a good list of musts already.
If you're in the area to see Munich, I'd think about going to Austria instead. It's in the same general region, the landscape is spectacular, the cities are all very pretty...Munich can offer you beer, tourists and a short trip to Dachau concentration camp.
Amsterdam is an interesting place - I think it's worth a visit.
Berlin seems to be THE place to go now. I went back last year for the first time in 25 years and still didn't like it at all. Ugly, dirty - lots of hipsters. If you're into military history it might be worth it to spend a few days there though - there's lots to see in that respect.
If you have a car I'd invest some more time in Italy. Fucking awesome country, great people, and if you can get away from the more touristy areas, the best food you've ever had. Driving around Tuscany - there are so many smaller places that you could just take your time exploring. And also in that general region, I've heard Slovenia is beautiful. I've never been, but everyone I know who has raves about it.
It doesn't look as though you're going to Northern Europe. My happiest memories of my first European trip as a backpacker was Sweden. That was a long time ago though and it sounds like it's changed for the worse.
Have fun man.