As a workaround, I've found this:
Annotate with Preview or GoodReader. On the iPad, GoodReader can extract the text of annotations, when you select 'view summary'. This summary can be saved as a txt file.
[Update: GoodReader seems to have removed 'view summary' in .txt format for some unfathomable reason. A workaround (at least for me) is to use the free service, Send to DropBox. You simply select 'email summary', and the annotations appear in a email message. Send this to your Send to DropBox mail address, and you have a .txt file with your annotations. In may ways, if you use DropBox, this is easier because it cuts out the step of uploading the .txt]
On OS X, I've downloaded Skim. I can open an copy of a pdf annotated in Preview or GoodReader, then convert the annotations to .skim format by selecting file>convert notes. Having done this, I can select file>export and there's an option to export notes as a txt file.
If anyone can come up with a more elegant solution, I'd be very interested to hear it.