Is JNT really a proprietary binary format?

Ok , couple of things first. Ink is ink and i would rather it stayed ink. That probably means i would rather have the actual serialized object . Thats where ISF shows up.
Ink Serialized Format (ISF) , the most compact persistent representation of ink is extensible with custom attributes (identified by a GUID) and allows you to store any kind of data or metadata as an attribute in an ISF stream.

Alright , and .....ISF is a format specific to Windows XP Tablet PC Edition, and the only way you can get at ISF is to use the Ink object's Load and Save methods.....

everything else starts after ISF.
For best performance and total control of ink ISF is the way to go with whatever enhancements you need to work with ink

For heterogeneous content, use fortified GIFs to encode ink into HTML documents. Browsers and html's hyper linking are your friend.
are required.

For Images you could move bitmap and metafile that are got from inks conversion to GIF

And we can alsoe encode ink in the RTF as OLE objects. This is very useful for pasting into an OLE container, such as Microsoft Word.

and of course the most useful format is XML .

the supported PersistenceFormat are and though it essentially is 2 formats , you can go anywhere from this. Actually go any where and come back ...

enum PersistenceFormat {
InkSerializedFormat = 0,
Base64InkSerializedFormat = 1,
Gif = 2,
Base64Gif = 3
};

based on the work am doing for WriteFree "the open source journal" , i think that the SDK persitence model is pretty well done, at least from a usability perspective. The frustrations that most users have with Windows Journal i believe are related to not being able to get at all of Journal programatically. We want access to the documents before they are created, after they are created and yes we want access to that Print Driver. We want this things and we want them now ;)). I think the SDK does a very good job at making it possible to built your own ink creation and consumption framework.
Journal design considerations probably sent it down the "proprietary" document format that it has. I am not sure its very proprietary.