For the basics (eMail, calendar, simple notes, etc.) I stay inside the OS X ecosystem: Mail, iCal, Notes, TextEdit, Reminders, etc. I'm not constrained by whatever limitations they have, and like how easily they work with each other and sync through iCloud. I have tried many alternatives, but find I'm happy keeping it simple.

As for larger tasks, I start pretty much everything in OmniOutliner, and keep track of tasks with OmniFocus. They're seriously well-made apps. And after years of DevonThink, I now use Evernote for logs, journals, collections, notes, etc. I liked DT's complexity and features, but Evernote is almost as fully-featured, and it's sync-capabilities to all my devices makes it far more useful for me.

I have tried several times to use Scrivener for starting and larger projects, but keep going back to OmniOutliner. YMMV.