Scrivener is an excellent application on Mac (and recently on Windows) for all sorts of long form writing.
Limited syncing with Simplenote and Index Card on iPad are supported but what many users have been craving is full synchronization with an IOS version of Scrivener. Dreams do come true as an IOS version of Scrivener is being targeted for delivery in 2012. It will be a universal app for iPad and iPhone and it will be very interesting what features are provided on the different sized screens with touch interface.