You'll notice that the tours from GAdventures and Intrepid Travel briefed below are small, limited to 12 people (at most 16).
In the case of the Select Italy packages, they're essentially private tours including lodging, guided walks and side trips each day, and often most of the transport from place to place.
No giant lumbering buses here. You travel on local trains, city buses, ferries, and the occasional private car or minivan.
Airfare is not included—though most of these companies can arrange it, often at discounted rates—leaving you free to find the cheapest fares on your own.
Also, none of these tours are "all-inclusive"—and that is a very, very good thing.
Most of the classic, "all-inclusive" tours out there offer the lowest common denominator of travel experiences, traveling firmly in the deepest ruts of the established tourist routes. Instead, these low-priced guided trips come with plenty of options to customize your days and your vacation can remain your own—only with the benefits of a professional guide.
With this kind of tour, some of the sightseeing admissions are included but some are not. That way you can pursue the activities that appeal most to you. Some in the group can hit all the museums, others go shopping, and others simply wander the medieval streets and maybe get a cappucino at a cafe.
Same goes for dining. I can think of nothing more depressing than being forced to eat all ogether at every meal (which mean diners only at touristy restaurants able and willing to accommodate large tour groups). Instead, with these tours you usually get most breakfasts, perhaps a special lunch or dinner or two (at an agriturismo restaurant, a group picnic, or eating the results of a cooking class), but are otherwise left to find your own wondeful trattorie and osterie (though the guide can always provide recommendations).
Still, for those who appreicate the savings that a larger, more traditional bus tour can offer, I've also included a few classic coach tours from Viator.com and City-Discovery.com.