With .epub support coming in Scrivener 2.0, some users here might be tempted to use iBooks on the iPad for proof-reading manuscripts. Notes and bookmarks have been recently introduced to iBooks in an update, so we’re almost there. Well, almost. For some stupid reason, Apple decided against an export feature for notes in iTunes.
So you can sync notes and bookmarks across multiple iDevices, but you can’t read them on your mac.
My guess is that the notes are stored in binary form somewhere in your iTunes Library file, which is in Apple’s closed proprietary ITL format. There might be third-party software to read this file (?), but I haven’t heard of a tool that deals with notes and bookmark data.
The good news is, that (provided that you have the right tools) the data can be accessed directly on the iPad or iPhone via USB connection. iBooks’ bookmarks and annotations are stored in the iOS file system in /Books/iBooksData2.plist. You will obviously need a third-party tool like PhoneView ($20) or DiskAid ($10) to copy the file, but no Jailbreak is necessary.
The plist format is really simple, so if anyone’s interested, I might give it a try and build a tiny tool to convert the data into something that can be reimported into Scrivener.