Scrivener
I was able to compile my manuscript in mobi format and ebook format easily. I checked each for formatting issues using emulators or online as I uploaded to sites I'm selling on. No errors! Even over at Smashwords. In fact, with only the one pass, I made it into the premium catalog!
Yeah. Scrivener is awesome.
Otherwise, Calibre is excellent for organizing ebooks. Haven't had to use it for tweaking yet.