You can, of course, save the contents of a Mail mailbox as an archive. But the messages in those archives can be read only if you import the archive back into Mail. What if you want to archive those messages as a text file that’s easy to read and search?
The solution turns out to be pretty simple: select the messages you want to archive (no need to expand message threads) and choose Save As. At the bottom of the Save As window, open the Format pop-up menu and select the Rich Text option. Mail will then save the selected messages (expanding threads as necessary) to a single RTF file; that file will include images and other attachments, as well as message text.
You can also select the messages, copy them with C-C, open a new RTF document in TextEdit, and paste the messages with C-V. Or another option you have is to save selected messages as Raw Message Source (instead of Rich Text), producing Unix-friendly .mbox text files.