I think the heuristic in common use is similar to this:

• If there are two line endings in a row, it's a new paragraph and they should be kept.
• If there's a quoting character at the beginning of a line, the line ending for the previous line should be kept. Quote characters include:
  • >
  • ::
  • name:
  • name>
  ... and any number of nested quote characters after the first without a line ending in between stay part of the same line.
• Otherwise, strip the line ending for side-scrolling or soft wrapping (or reformat the lines with a new hard wrap to the maximum length the client sets).

You'd have to do that with the data after you've already retrieved it from the POP3 server. The protocol itself is just a text dump and is not concerned with formatting in any way other than standardized line endings and a blank line between headers and the body.

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