The name "S.S. Minnow" was actually named after Newton Minow and was chairman on the FCC in 1961. He made a speech and called television "America's vast wasteland." The boat was named after the man who, Sherwood insists, "ruined television." Minow gave networks authority and placed the power of programming in the hands of the networks. He did this after Gilligan's Island was started.

There were actually four S.S. Minnows used on the show. The first Minnow was purchased and towed out to Kauai and used in the beach scenes.

1) Gilligan - Willy Gilligan
    (Never used. Bob would have argued NOT to use Willy, preferring JUST Gilligan)
2) The Skipper - Jonas Grumby 
3) Thurston Howell III - Thurston Howell III
4) Mrs. Howell - Eunice Wentworth (Lovey) Howell
5) Ginger - Ginger Grant
6) The Professor - Roy Hinkley
7) Mary Ann - Mary Ann Summers

We filmed 98 episodes in three years.

The pilot episode was filmed on a real island - the northern island of Kauai in the Hawaiian chain. The actual series was filmed at CBS Studios on the back lot, where they built a lagoon especially for the series right next to the Hollywood Freeway. We also worked on a soundstage, covered in sand and loaded with palm trees. That's where we had all the huts and our dinner table.

Why did the theme song say 'and the rest' the 1st season?
It was a contractual thing that first year - Russell and Dawn's contracts for the show didn't specify that they would be credited up front with the rest of the cast. Obviously, since the question has been asked, all of you realize how ridiculous it was to have 5 of seven cast members mentioned at the beginning of the show, and the remaining two referred to as 'and the rest'. Happily, that was corrected the second season and they were included in the opening credits just the way they should have been from the very beginning of the series.
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On November 15, 1963 Bob Denver and crew arrived in Kauai, and 
from Nov 19 - 22 they shot all footage in beautiful Moloaa Bay. There
is only one vacation house at the film site and YOU can stay there!
(Providing you have deep enough pockets, that is)
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The pilot and the first episode were filmed in Kauai located in the Hawaiin islands. The crew had looked at locations in Los Angeles and Catalina Island but found them to be useless. Los Angeles had no tropical settings and Catalina didn't have any palms trees. They finally found their island.... Kauai!
Note: The first episode proceeding the pilot was filmed at Zuma Beach near Malibu, California, mixing in a little footage from Kauai.

When they arrived in Kauai on November 15 1963, Bob Denver and the crew stayed the night at the Coco Palms Hotel near the southern end of the island in Wailua next to Kapaa. Elvis also stayed there while filming "Blue Hawaii." That resort has been closed since Hurricane Iniki, but people are allowed to tour it by special arrangement, usually with a tour or wedding.

The next day, they moved to a location closer to the film site at the Hanalei Plantation Resort in Princeville, overlooking Hanalei Bay (where South Pacific was filmed). In fact, the production designer of South Pacific designed the Hanalei Plantation and its cottages. The Hanalei Plantation consisted of a large main building with a series of small cottages leading down a steep hill to Hanalei Bay. The main building was for the crew, and the small cottages were for the cast and executives. The land which held the Hanalei Plantation Resort became a Club Med for a few years. The Club Med eventually closed down and was torn down. Someone started to build condos there, but lost their financing after pouring the foundations. It is now totally vacant except for those foundations. Two years ago, Disney tried to buy the property, but a deal was never put together.

Moloaa Bay was the filming location, and the scenes were shot in only four days from November 19th through to 22nd, 1963.

While on Kauai, they realized that they needed a boat (the S.S. Minnow). Since they couldn't find a suitable boat on the island, they had to look elsewhere, and finally found a boat in the Honolulu Harbor. Once the Minnow was towed to Kauai, the suits got to work and punched some holes in the hull using a couple of sledge hammers. There were four Minnow's used on the show, this one seen beached on the island. After filming was complete on Kauai, the crew relocated to the Honolulu Harbor where they rented a boat (S.S. Minnow number 2) and filmed the crew boarding and sailing it out of the Honolulu harbor. Another Minnow was used when it fell apart from Gilligan's pancake syrup glue. The last Minnow was used during the opening theme of the second season sitting in the lagoon and was constructed just for CBS Studios in Burbank California.

The best way to see the site where Gilligan's Island was filmed in Kauai is to take a tour. Bob, the President of Hawaii Movie Tours has a great package! They'll take you to the filming location of Gilligan's Island and even bring out TV's and show you exactly where each scene was shot! Amazing! They supply food and a lot of fun as well!