I just use notes on my iPhone/iPad/Mac for when ideas and dialogue pop into my head. I need to get them out and down as quickly as possible, so I don't forget them. Once they're written, I can ruminate on them for a few weeks, and make edits as I do so.
My 'main' writing program however, which I use less often but is where the 'serious business' writing happens, is Scrivner. I absolutely love that program! I write in snippets, all out of order, all over the place, involving whichever character is occupying my thoughts at the time. Scrivner helps me take those snippets from Notes, apply them to folders for the characters involved, and add extra tags for searching.
It also has a fantastic comic script template, which speeds up dialogue formatting enormously!