I'd have to agree with you. The Magnificent Seven storyline is one of my favorites. I loved all of Cool Ranch for that matter. I know I'm in the minority in the sense, but there's just something I love about the whole atmosphere.
Wow, that's such a hard question to answer! There are so many great parts in this story.
Although it's a bit cheating (because it is so encompassing), my favorite parts are the ones with the Armada. I love the Armada (well, not that way... I love them as villains); they make such a chilling and formidable enemy. I especially loved being terrorized by Deacon (!) and later Kane (!!). The times were I wasn't expecting them to pop out of nowhere (or drop bombs on me! in the case of those Dragoons in Marleybone) were the best.
Some other favorite parts that come to mind: -- The Monkey's Paw, which beautifully mingled horror and pathos (I even shed tears for the terrible but ultimately redeemed fate of the winged monkeys) with great Poe-like atmosphere. I think Poe would have approved, along with Mary Shelley, Ann Radcliffe (the real one, not me), and all those pioneers of the genre.
-- Death & Captain Blood: I particularly liked the riff on the famous folk-tale motif 'Death is tricked by..." It was also an excellent, absorbing story.
-- Bonnie Anne' promotion quests #2 & #3.
-- Beach head. Boy that really jazzed me up! And the Wreck of the Victory. I suppose really this is covered by #1 above, but Marleybone in general was really a favorite.
-- The Valencian Throne Room. Yes, it's covered by #1, but I really liked that sudden surge of "huh? What??!!" I got the first time playing it. We had been set up very nicely by not even seeing an Armada clockwork until then!
-- Coming up with Aegilles Triumphal Feast (and how I laughed at its conclusion!)
-- All the poetry references, particularly the Shakespeare ones -- especially the 'performance' of Pyramus & Thisbe
And there are so many others! It sure has been a great game to play and story to enjoy.