Whats your reason for going to Frankfurt?  I suggest skipping it and going to Prague instead. 
 
If I were you I wouldn’t really bother with setting a definate time frame for your itinerary.  Maybe you’ll want to book your accomodation for the first week or two (and of course for oktoberfest), but I don’t think accomodation will be filling up.  Then you have the freedom to go anywhere, anytime.  Personally, I wouldn’t want it any other way.  Some of my best memories have been on a whim. 

I agree here with rob to add prague to the list.  In belgium ill visit Brugge instead of brussels, really not much to do there. Just like Zurich, i think Lucerne will be way better but its just my opinion.
 
Have fun!

Sounds like you’ll have a nice trip.  Take lots of money – the cities you’ve selected aren’t cheap!  Agree that Brussels is less stay-worthy than Brugge.  Agree on dumping Frankfurt, maybe Luxembourg and Vienna (yawn), Zurich (yawn, yawn.)

It does seem that your itin is very heavy on the megacities.  You are seeing so many of them they’ll blur together.  They’re pretty expensive places too, as a rule.   Break it up with some visits to smaller places where you can chill a bit, see something different, and save a little $ on accommodations.  Ideas:

Paris:  head north to Caen and Bayeux, see Normandy’s D-Day beaches.

Amsterdam:  see Volendam, Marken, Monnickendam, and especially Zaanse Schans to the north; head west to the beaches?

Germany:  Berlin and Munich are great, but between Brussels and these cities be sure to see the Rhine and Mosel River valleys – Trier (Roman ruins), several medieval castles you can tour (Burg Eltz and Reichsburg in Cochem, Marksburg in Braubach.)  Good subsitution for Luxembourg.  You’ll be there during wine harvest festivals – lots of unusual fireworks shows on the Rhine over the weekends in different towns, with “burning” castles and the like.

Salzburg – get over to Hallstatt for a day, maybe Berchtesgaden.

Bern:  get to the mountains quickly – Interlaken, Lauterbrunnen are good bases.  Go to the top of the Schilthorn for a view of the planet.

Italy:  Florence isn’t small but it is pretty wonderful.

Ya we would love to go to Prague. However, its not one of the places that you can go for free with the rail pass, and in the interest of saving money we are kind of on the fence about it…does anyone know about how much it would cost from Berlin to Prague?

my wife and i are planning a similar trip in april and too are looking for less expensive smaller places to visit which we are finding hard to sniff out since we are canadian euro rookies, anyways i would definetely recomend prague (the only euro city i’ve been too) we’ll probably get the following pass which has a prague excurion ad on for 60 see here http://www.eurorailways.com/rail/mcp/eurail/fp.htm

The czech rail site, www.cd.cz says a ticket from Decin hl. (first stop inside Czech republic) to Praha hl. costs 162kc, which should be about $8 USD.  But it will probably be slightly more expensive because you’ll buy your ticket from the german border. 
 
The money you’ll save in Prague vs. say..Vienna, in cost of food, beer, accomodation, and anything else you buy, will probably make up for the price of the ticket.