The rail pass is great... depending on your schedule, you might get a fair bit of mileage out of your travel days as well. Assuming you like thinks hectic, as I do. IMO if your travel time is under ~4 hours, you've got a lot of time to do things on a travel day.
If I were you, I'd try to get to Paris as soon as you land. You can spend time in Amsterdam at the end (and it's a great place to end your trip, as it's rather unique).
Paris... a must see city IMO, if a bit touristy.
Nice... never been.
Nice->Rome... that's skipping a lot. I would add Cinque Terre (takes a full day to see all five villages, but no more than that - book 2 nights in La Spezia), Florence (for me, not too interested in the renaissence art museums there but it's a gorgeous city - especially if you walk around at night, day and a half is good for me), and if you're on the rail pass you can make a half-day trip to Pisa as well, or stop there between La Spezia and Florence.
You might also want to consider adding the Naples area... stay in one place (I stayed a Fabric in Portici... nice hostel) and hit up the likes of Pompeii, Hercolaneum, Capri, Sorrento, Vesuvius and the Amalfi coast (if you get sick on buses, take the boat - if you get sick on boats, take the bus, if you get sick on both, skip it as Cinque Terre is similar and you'll enjoy Cinque Terre more.)
To manage your travel times, you can skip cities on the way up and down... e.g. Nice -> La Spezia -> Florence via Pisa -> Naples -> Rome -> Venice.
Vienna... I'd skip it.
Munich... wasn't on my radar, kind of a last minute thing. Man, I regret that. Anyways, if you have the rail pass, Neuschwanstein is a day trip and you can get there free. Can't really help more than that.
Munich -> Amsterdam ... this is a long trip, might want to break it up with a stop in Koln... the cathedral is right by the station. If you're into Koln late though, might as well continue to Amsterdam.
Anyways those are just my thoughts, but this will be your Bible, it's the Eurail timetable:
http://www.eurail.com/downloads/eura...ins-europe.pdf
The map is a bit less important, but it can help you figure out efficient routing.
http://www.eurail.com/downloads/eura...l-map-2010.pdf
The travel time map is helpful for preliminary planning, but be aware that you can't just add them up... that's why the timetable is your best bet.
http://www.eurail.com/images/eurail/...times-2010.png