I've found that ezPDFReader works best for me on my M96, because it embeds the annotations in the PDF itself (perhaps the built-in reader does that as well, but I didn't want to take any chances). Response is quite fast, in my usage at least. Regarding a notebook, I've used Quill, which is open source with an open file format (but isn't really maintained any more, and has a tendency to crash on my M96) that can easily be exported or converted to PDF, or Papyrus, which allows for automatic export to PDF and uploading to cloud services, so I know that I won't be stuck in a proprietary format.
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