as a markdown fan myself, I've been using ByWord / TextWrangler and PanDOC for most of my creations lately. but this is post writing, turning into ebooks / books. For writing, ByWord and Scrivener are my current choices, especially now Scrivener has joined the iOS team.
I know lots of writers, and there is no one answer for this. Most simply use Word. I've used quite a few apps, from Scrivener, StoryMill, Word, WordPerfect, Byword, MacJournal and Evernote... mainly because I am a nerd. =) but in the end, you could write a book in Text Edit if you had to.
This pretty much sums up the entire thread. I don't know if there is such thing as a "best writing app" since what some may consider best is utter garbage and vise versa. I would try out all the writing apps you can find until you discover one that meets your needs.
I am just starting to scratch the surface of Scrivener and I am really digging it so far.