I have 3 days. We are flying into Zurich, then taking the train onto Basel to get on a cruise ship. How and where is our time best spent???

I think that Basel has more to offer in terms of museums. It has an interesting music museum in a former prison, a historical museum in an old mansion, the Fondation Beyerler for contemporary art, the Vitra chair collection in near-by Weil housed in a Frank Gehry building, as well as a fine arts museum (we only saw a special exhibit on Soutine when we were there, so I can't speak of its over-all collection).

http://www.flickr.com/photos/mksfca/...th/4206988010/

Zurich is primarily a business city so I wouldn;t stay there and IMHO Basel is quite boring. You need to get out into the mountains if you want to see the best of Switzerland. Head for Lucerne or Interlaken for a larger town - or to one of the smaller towns actually up in the bernese oberland.

I agree with nytraveler's recommendations. Skip Basel and Zurich and head to the more interesting places to see. Both, Lucern and Interlaken are an easy train ride from Zurich. Zurich airport has a train stn and you can take a train from the airport directly to Lucerne (not 100% about Interlaken).

Maybe you should tell us what you find appealing about Zurich vs Basel?

I enjoyed Basel quite a bit.

Are you arriving from North America at ZRH in the early morning?
You could easily take a train directly from the airport to Luzern (trip will be about one hour 15 minutes), spend the rest of the day there, and overnight. Select one of the lake cruises with combination ticket to Pilatus, perhaps. Or Rigi. Wander the streets and the covered bridges. Find a great dinner.

The next day, take the train to Basel (again, the trip is a bit more than one hour) and discover this small city. Great museums, as Michael notes. I especially enjoy the Beyeler Foundation.

http://www.museenbasel.ch/en/index.php

Pedestrian-only areas to stroll, interesting architecture, open air farmers market, a cathedral that dates to the 12th century, near-by Roman ruins--you'll find plenty to do.

http://www.basel.com/en.cfm/baselinfo/

If you do decide to spend one or two nights elsewhere before going on to Basel, you might think about splitting your 'stuff.' Take a small bag with essentials with you on the train. Use the baggage service of SSB to take your cruise luggage to Basel and pick it up at the station when you arrive there. (The office for checking in the luggage at ZRH is right next to the windows where you purchase your train tickets.)