This seems like a good thread for me to add my first post
I use Eaglefiler for taking notes / organising information on my mac, it doesn't store files in a database so apparently doesn't suffer the slowdown you get when using something like Together, (I've not got that much stored in it yet so I can't verify this personally).
For iPhone notes I use Elements and sync the Eaglefiler files folder via Dropbox. As I mostly use plain text with markdown I can edit files I've created in Eaglefiler in Elements.