I've taught a bunch of Storylines but my top three favorites were our ocean voyage to the islands of Hawaii (a science themed oceanography, marine life, volcanoes, geography and persuasive writing focus), our Native American potlatch (social studies, cultures and narrative writing story) and the Rainforests at the Crossroads JASON Project Expedition storyline (science, organisms, expository writing, math, and technology story).
My favorite Storyline was the rainforest of Panama. I was selected one of the eight teachers to actually travel with Dr. Ballard's JASON Project expedition team and 24 students to live and work in Panama for two weeks at the Smithsonian Tropical Rainforest Institute. The student argonauts were responsible for conducting real science in the field with real scientists and then hosting the live broadcasts that were satellite-fed to museums around the world. Students who were using the program came to the museums to watch the live event.