In southern Europe it doesn't seem to be a problem, with the exception of Greece. We fly in to Lisbon a lot because we like SATA airlines from Boston, and there is no hassle in Lisbon, in fact, we have had an immigration officer tell us not to worry, just stay out of other trouble. Same in Rome flying in, in no one has looked at our passports since we got to Italy more than a year ago. On the other hand, we have heard tales of a few problems in Greece, including fines, but also know several cruisers who just went, over the 90 day limit, and had no problems. We are headed for Greece next summer, but we should be in compliance when we enter due to the winter in Vermont for Wanda to recuperate, and once we are in the islands I don't think anyone will be checking.
We understand it might not be good to fly into Brussels, Germany, perhaps France, and Greece. Holland is probably OK, we haven't heard anything. If you are in Holland next year we might be able to stop and say hello, as we want to head north with our camper, see a German Christmas fair or two, and then, perhaps after some time back at the boat in January and February, be in Holland for the tulips in the spring.
The US cruisers we meet seem to be divided into two camps, those like us who just don't worry, and some we meet who worry too much and miss out on some of the Europe experience because they spend a lot of time back in the US. I think even in the countries that might care, if you enter the country in compliance and don't fly in and out a lot, you will be fine. I will say we have trouble trying to research all the various angles to find a definite answer, including temporary residency, an extended visa, etc.
Also wanted to say I went to your blog after reading your post, and certainly enjoyed reading about your travels, especially Flores in the Azores. We had the same tour guide, and have difficulty thinking of a more beautiful place.