Unfortunately the 3 locations you have selected are extremely popular with tourists and are still quite crowded in September. We were in Dubrovnik in later September and on one of our days there were 5 cruise ships discharging their passengers into and filling up the town.

What do you want to do in these locales? If you want to see the famous sights, so does everybody else. At least if you stay in the historic centers, you will have early mornings and evenings free of daytrippers. If you stay out of town and daytrip in, you'll be there with all the crowds. You could stay out of town and just see what's to be seen there.

How many days total do you have? Have you allowed for travel time in between? 3 days each is 4 nights. 3 nights is about the minimum apartments will rent for. Except maybe sobes in Croatia.

If you want to avoid tourist areas then you have to avoid the tourist sights. In Venice, once you leave the Rialto to St. Mark's trail you will find fewer tourists. Old Dubrovnik very small and is full of tourists. It would be a shame to avoid the old city just to avoid tourists.

If you prefer the routes less traveled then you should avoid these three cities and find small, out of the way, places to visit. There are tons of towns in Italy & Croatia that never see tourists. I'm sorry I don't know what they are but you can figure it out by looking at a map and consulting a guide book. If the town you choose is not in a guide book and doesn't have much internet information then you can bet you will avoid tourists.

Visit St. Mark's square early in the morning and later in afternoon/evening.

Yes, all three of these cities will be filled with tourists, and you can count yourself among them! Places like St Marks Square will be crowded with tourist, but don't skip it... that is what you are there for! It will be obvious to you which places are so "touristy" that you want to avoid them. For restaurants, just don't eat in the first place right next to any major sight. In all 3 of these cities, if you walk a few blocks away from the main crowds, you'll find decent restaurants and quieter streets. Order local foods and drink local wine or beer. Get lost in the backstreets. Have fun, and accept the fact that you are a tourist too!

If you want to avoid the tourist hordes and the high seasonal prices, let me suggest a new itinerary for you:
Ljubljana, Slovenia
Bassano del Grappa, Italy
Bevagna, Unbria

Face it---the others are touristy for a reason.

I would skip Florence unless you are serious about art. It is essential then, of course, but it is always a zoo in the historic center. If you want to hang out and absorb the flavor of Italy, a smaller city will work. BobtheN suggests several above.

Bassano may be full of Germans or Austrians but it is a very pleasnt place. Siena is a lot easier than Florence and just as historic and even more spectacular in some days, and you can go to Florence for a day trip.

But I would follow msteacher's advice, suck it up, admit I am a tourist and enjoy it. There is a reason these have been tourist centers for hundreds of years.

Agree to leave the major tourist sights for early n the am or very later afternoon - when the mobs from the tour buses will have departed.

However, you are in major tourist centers and there is no way you are going to avoid other tourists completely.

I appreciate all your insights. However, I feel the need to clarify. I do realize I am a tourist and am going to tourist heavy destinations, I am not looking to completely avoid tourists. I was looking for recommendations of little gems that people have found in these cities. Like restaurants, cafes, B&B's, shops and the like. I have been to tourist heavy cities (NYC, San Fran, Paris) and have gotten recommendations of places people have been that most tourists are not aware of.

I will definitely take your suggestions into consideration. Thanks again!

Dubrovnik was probably the most crowded, touristy place I have ever been. I doubt there are ANY hidden gems. Still, it is one of the most beautiful places I've been so 'worth' going to. My tip would be plan to be out and about early and late - the cruise ships only tend to be there from about 9-5. So walk the walls as soon as they open or in the late afternoon, early evening. We took day trips to Mostar one day, and Montenegro the other so were not there mid day except one day and that worked well for us.

Venice - it's most crowded around the Rialto Bridge and Piazza San Marco and the route between them. Go to those areas early and late and mid day just wander a few 'blocks' away and you'll likely be all alone. Venice has the same cruise ship mid day tourist uber-crunch as Dubrovnik. But really they must be afraid of getting lost cause most of them are in that relatively small area.

But both of them are so unique, so wonderful - just plan your days and times to avoid the worst. In Venice certainly do not eat anywhere in sight of the Grand Canal - prices much higher, quality lower. Although now that I think of it, there's a cafeteria type place right next to the Rialto bridge that was really not bad. But in general....

Florence - more or less the same advice, around the Duomo and Pont Vechio are the worst. But I agree with bob's advice, at least on this one, you could find other charming mid size Italian cities with wonderful sites that are at least a bit less crowded. In fact Padua, right next to Venice, is a great city and very untouristy compared to the others. Verona also great but more tourists there, although less than Venice and Florence.

You may be 30 years late. You can blame the tour bus/ship industry.