Like Bob said, the list is pretty much endless, but I do have some favorites. All of our cruising in the Inland Passage area has been above Prince Rupert & by far the most of that above Petersburg. I think the further you venture north the more wildlife & less people & boats you will encounter. If you venture off the main Inland Passage cruising routes of this area it will be even more so with the outer coast of Chichagof & Baranof Islands being the most remote, beautiful & wild of all. Of course the risk factors increase & have to be accepted the further you venture from the main routes.
I will provide a short list of my favorite towns & places to see but what is fantastic to me might not do much for you, so my advice is do what I did prior to all our cruises & that was spend many hours reading the cruising books such as the Douglass-Hemmingway, Exploring Southeast Alaska. I didn’t know about the C-Brats on our first few Alaska cruises so no information there for us, but with you I think the Grand Adventure Forum to be invaluable. Many cruises of the Inland Passage & Southeast Alaska are recorded there in detail in a 22 CD. I alone have written about the four of ours in 03, 04, 07 & 10. If you have already read them then great, but I would read them all again if your plans were mine.
Favorite larger towns & Marinas would include, Skagway, Haines, Auke Bay, near Juneau, Sitka, Wrangle & Petersburg. Small towns; Elfin Cove, Pelican, Tenekee Springs & Port Alexander.
My favorite of all cruising areas, are the area around Elfin Cove & Pelican including Dundas Bay, Lisianski Inlet & Strait & the outside water of Chicagof Island from Lisianski Strait to Khaz Head. The bays on the south end of Admiralty Island with Gambier Bay being foremost. The Inlets & Bays off the east coast of Baranof Island, Chatham Strait with Red Bluff Bay being foremost. Holkam Bay, which includes Tracy & Endicott Arms which in turn have North & South Sawyer & Endicott Glaciers & Fords Terror Inlet. Have seen more whales in Fredrick Sound & Icy Straight than anywhere else in Southeast Alaska. Heaviest bear concentrations near Pelican & Hoonah with the most at the head of the bays on the outside of Chicagof Island. There are many areas with the bears more active & numerous than Pack Creek & without the restrictions & having to pay to see.
We have never cruised Glacier Bay & I don’t plan to so in the future. Far to many restrictions on small cruising boats there for my taste, with tide water glaciers like those in Tracy Arm able to be accessed without the restrictions in equally beautiful settings & wildlife just as abundant or more so in many other areas.
Jay