Melk Abbey or Budapest.
 

Day trip from Vienna on the Danube--which would you choose.

Melk Abbey, try to catch it during an organ concert, it is amazing. Take a climb up to the organ and stroll the other rooms, I really enjoyed it.

Budapest is nice too, hard to choose, depends on your taste, really.

Budapest need more than a day. Save it for another trip.

weaverm: There really is no comparison. Budapest is an amazing beautiful city with much to see and do, but it requires a minimum of three days to do it justice and more if you really want to see it.
Melk would be a much shorter ride, has a pretty fantastic Abbey and the town is cute. It is a neat place for a one day/night trip from Vienna. Take a boat on the Danube up to Durnstein or Krems, both neat (if a bit touristy) towns. You can train or boat back.
Trains leave Vienna for Melk hourly and it takes an hour. The Hotel Furst is a creaky, fluffy old hotel (Rick Steves accurate description) right under the Abbey. It is clean and quaint. Try to get one of the upper level rooms right over the front with a view of the happenings below. The restaurant in the hotel serves medium-priced home cooking. Really quite good. Have a great trip.

Thanks for the help--we'll do Melk and vicinity this trip, Budapest next trip.