Large-ship alternative
Princess Cruises' 670-passenger Tahitian Princess may well be the only other vessel to visit all three archipelagoes (11 days; departures October 11, 2007, through February 8, 2008; from $1,229), and it includes an overnight on Raiatea. Just be sure to book far in advance so that Kleon Howe, of the Art of Travel in San Diego, can reserve each island's top guide for your private shore excursions before the cruise line snaps them up (888-294-3598; info@theartoftravelonline.com; theartoftravelonline.com).

Indonesia
Top Itinerary
"Secrets of the Archipelago" on Geographic Expeditions' Silolona
Length 14 days
Departures March through October 2007 and from May 1 through November 15, 2008
Cost From $17,745
Map Click to view

The distances in Asia are so great that the only way to find a port-intensive cruise itinerary is by narrowing your focus (for our all-around favorite Asia itinerary). This itinerary covers some of the least known Indonesian islands, starting with Flores. Here, up to 13 guests board a tiny, black-sailed phinisi schooner, a modern vessel built according to an ancient design. Though close to Bali, Flores and the other Lesser Sunda Islands have distinctly different flora and fauna, since they were never connected to Asia (as Bali once was). You'll spend the next two days among the 600 islets of Komodo National Park, a World Heritage Site uninhabited save for two villages. The sea life in the area—from the isolated, pristine reefs to the giant mantas, whale sharks, and enormous schools of tropical fish—is as impressive as its famous landlubber: the nine-foot-long Komodo dragon, which you'll search for with the guidance of a park ranger. From there, the Silolona sails to Sumba, source of the ikat fabric found in many museums and private collections. On both ends of the journey, guests also spend two nights at a private villa in the highlands of Bali, where rituals and offerings are part of daily life and nearly every day is a Hindu festival.

How to book
Call Katherine Doty of Geographic Expeditions in San Francisco (800-777-8183; kate@geoex.com; geoex.com).

All prices are per person, double occupancy; early-booking discounts are often available.