I would recommend either plain text or XHTML 1.0 as your format. sbmlexport will export both of these to SBML as XHTML 1.0, which is what SBML documents as the intended format for Notes. These are also the only two formats that the SimBiology graphical interface understands.
That said, if you're not using SBML or care about the appearance of notes in the graphical interface, you are free to use any format you find convenient.
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