Tour Company: We booked with Gate1 and their '13 Day Kaleidoscope of Central Europe'. We researched this out fairly well and concluded it was the most 'bang for the buck'. In hindsight, we were pleased, even though we felt rushed at times. As with all these tours, there are up to 50 of you on one bus. With any luck, it'll be considerably less and you can spread out a little.  Again, with wonderful clear hindsight, I would unhesitatingly tour Central on my own with a good guide book and using local tourist offices. I'm doubt you'll save that much money, or have it as convenient, but you'll be more in control of your own schedule. After all, finding and reserving hotels and restaurants takes time away from your adventure, unless you enjoy that sort of thing. 

Guides/books: As usual, I try to study an area before going, but found little suitable in our library under 20 lbs. In desperation, I grabbed a Rick Steve's Eastern Europe and found it a marvelous compact guide that including a little bit of everything from history to major attractions, self guided walks and the best shops.

Crime: We'd had plenty of warnings about crime, pickpockets, I.D. thefts etc. Not once did we ever have any problems. It's hard to feel unsafe when you see well dressed young women walking every were by themselves at all hours looking completely at ease.

Language: English is the official second language and it is difficult to find someone who doesn't at least speak a few word of it and most of the younger people are fairly fluent. Mostly as these countries are too small to expect foreigners to learn theirs, so they learn ours. Lucky us.
Tours and History lessons: Many of the tours will take you to an area, have you stand in one spot and then give you a 10-20 minute history lesson. Some of these spots can be a feast for your eyes, while others may be a simple statues of their heroes or a corner wall with bullet holes. You're not going to remember the lesson and but you won't forget that wall you stared at for 20 minutes. We like tours that keep you moving through interesting areas with light historical commentaries, so choose carefully.

Auschwitz: We didn't take the tour. It was one of the more controversial ones and I thought I'd mention my reasoning. Many people inc. Rich Steve's said don't miss this one and he gives it his highest rating of three stars. People who have taken the tour have said it was one of the most moving experiences of their lives. They're probably right.
First, it was costly, time consuming, involved a bit of driving and took away from other sights. Second, the war atrocities by Hitler (and somewhat Stalin) had been drummed into us on every tour prior to this. Third, when I was young, I remember seeing a man's face up close just after a severe accident he may not have lived through. That too was a moving experience that can yet haunt me if I let it. While we should never forget the lessons of the holocaust, I would prefer to see beauty instead. Your choice.

Crowds: Vienna is a beautiful city with a wonderful old section filled with history and art. Unfortunately it was cheek to jowl in so many places, we couldn't see anything but the top of buildings... even in late September. The same can be said for parts of Prague so you might want to take this into consideration when booking your trip.
Cost: Overall we found your dollar goes a little further here than it would in the USA, but not by much. Most of the countries have their own currency, but two have the Euro. Atm machines were available in all tourist areas of all cities we visited. Use up your coins as the banks won't exchange them.

Cesky Krumlov: in the Czech Republic Is one of those charming medieval towns almost too fairy tale like to believe. If you're anywhere near the area, it's definitely worth a day, or two of just walking the streets. I looked online and if traveling independently, rooms or Pensions can be had for under $100 right in the city center.

Housing: Trying to get some idea of living costs, in Vienna I asked our local guide what a house costs.
She explained that she didn't know as 85% of the people live in apartments. Since they're state owned, from the communists times, they just up prices every year to keep with the market and inflation.. sort of. It seems that a two bedroom apartment goes from somewhere around $500 to $1000 per month depending on the desirability of location, or less than half of what we pay here. Plus many don't own a car as the city is so compact, everything is within walking distance, so two of their biggest expenses are taken care of, plus they get exercise.