We flew from Prague to Budapest to avoid the really long, boring train ride. The cost was low - but it was several years ago - you would have to check.

Too bad your tickets are booked already.

I would have suggested flying into Budapest, then onto Vienna by train, then to Cesky Krumlov by shuttle for a night or two before moving onto Prague by bus or shuttle (before the Isreal part of the trip).

Maybe you could check into how much it would cost to change your tickets?

Highly recommend a night or two in Cesky Krumlov!

If you are absolutley tied to your current schedule, I'd fly from Budapest to Prague. But, try to do at least a daytrip to C. Krumlov!

Someone on a thread a bit ago said they rented a one-way car from Prague to Budapest and the one-way drop fee was only about $150. If that is still true, it's not a bad option from Budapest to Prague and allows you to drive to C. Krumlov on your way to Prague!

we also love chesky krumlov if you can fit it in without sacrificing a nice soak in the budapest baths!

Thanks everyone! This is very much an itinerary in progress so I appreciate the suggestions. I really like the idea of going to Cesky Krumlov, sounds like a fun way to get to Prague and out into the countryside instead of just big cities. So I think we will forget about Budapest and go to CK from Vienna, most likely train to Linz and then shuttle to CK. Joannyc - Yes, we are tied to flying into Vienna - business class frequent flyer award travel through United - fantastic!

we took a little van/shuttle between vienna and CK. i believe the left CK from the youth hostel... but it was very nice and comfy. i think it will pick you up in vienna from wherever you are staying (since they dropped off at our hotels.) might be easier than a train, then shuttle.

Thanks for the tip kawh, I'm thinking an overnight in Melk, then 2 nights in CK. Looks like a shuttle can pick us up in Melk, which does sound easier than train AND shuttle

I hope you would reconsider and not give up Budapest so easily. From Budapest you can take train to Linz, Austria, then take a one-hour or so shuttle to CK.
Two shuttle companies between Linz and CK are mentioned in this Linz's wikitravel page under the "By Bus" section:
http://wikitravel.org/en/Linz

Several years ago we started in Prague, traveled through the Czech Republic with a private guide/driver based in Prague, and ended up in Bratislava where we took the hydrofoil to Budapest and then spent a great week in that beautiful city. Among the more memorable overnight stops in the Czech countryside were Mikulov and Cesky Krumlov, which you should not miss. Alternative to Mikulov, there are other wine regions in the vicinity. We stopped at a wonderful, off the beaten track castle, en route to Mikulov, following the road along the border between Czech Republic and Austria - Vranov Castle in Vranov nad Dijy. I encourage you not to cut out Budapest but don't ignore the beautiful Czech countryside either. You might contact the guide we used (Katarina Kruspanova) (her webside is www.prague-perfect.cz). She might be able to pick you up in Linz and drive you to Cesky Krumlov and then on to Prague.

Going out on a limb here, but assume if you are going to Israel that you are interested in Jewish history? Strongly suggest you keep Budapest in your plans, as the Dohaney synagogue, the Raoul Wallenberg sites and other Jewish history is very interesting in Budapest. Prior to WWII, Budapest had one of the larget Jewish populations in Europe and there are many historical sites worth visiting.

We traveled in July from Budapest to Vienna by train then hired a driver to take us to Prague via Cesky Krumlov. Couldn't recommend more than a day there, but would highly recommend the service we used, mike-chauffeur.cz/. Mike is very knowledgable and would be glad to help you. He picked us up in Vienna.

Definitely would not cut days from Budapest or Prague for Cesky. If you're really interested in Jewish history, you'd schedule a day trip to Terezin from Prague.

I agree that Budapest...to Vienna ... to Prague is the better way to go.

Thanks for the advice everyone! For this leg of our trip, I ultimately decided on 6 nights each in Vienna and Prague in a nice apartment in each city, with day trips out of these cities for a change of pace. Will look forward to seeing CK and Budapest on another trip.