My nephew is studying abroad in Berlin. We wanted to know of anyplace to stay in Berlin and what would be a MUST see in Berlin for the two or three days that we would be there.
We would also take a flight from Berlin to Rome and stay there two nights. A train from Rome to Florence, and visit Florence for two nights, and then fly back to Berlin.
I know what to see in Rome and Florence - but no clue about Berlin.
Any tips?

http://wikitravel.org/en/Berlin

I suggest you only visit Rome with the short time. Or fly non-stop to Bologna and head to Florence [30 minutes from Bologna Centrale]. There are no non-stops from Florence to Berlin. Alitalia has one taking about 4.5 hours with a change at FCO.

RyanAir flies Naples to Berlin.

Do you have to return to Berlin after visiting Italy? Are you returning just to fly home? If yes, it might cost about the same for multi-city flights from home to Berlin, and then Italy to home. Find a cheap flight for Berlin to Italy.

Plenty of must sees unnerving. Open a paper guide and make a selection.
I think Fofors do print guides.

What time of year are you traveling? What is your budget for lodging and do you wish to be close to where your nephew is living. How many actual nights are we talking about here for your trip? It looks like you are spending one full day in Rome and one full day in Florence. An open jaw into Berlin and out of either Rome or Florence would save you some time.

One full day in Rome won't even allow you to scratch the surface. If you try to cram the Colosseum and the Vatican Museums (with the Sistine Chapel) into that one day, it will be crowd-overload torture.

I agree that if you're returning to Berlin just to get a flight home, you should instead buy a multi-city air ticket that would allow you to fly home from Rome.

mis they have nixed the Rome idea. The flight is from NYC to Berlin from March 6 to March 13. They need to have a hotel in Berlin for March 7, 8, 9. Then I have to get them a flight to Florence where they will stay two nights. My nephew is staying in Berlin Berlin whatever that means - that's the address
Gneisen Strasse

So I need reasonably priced hotels for Berlin and Florence.

Two nights is just one day. I'd suggest they stay in Germany - lots to see and do there and they won't waste so much of their precious time in transit. Is one day in Florence worth the cost of the plane tickets and the loss of a day of sightseeing in Germany?