I use "fetchmail" to retrieve my e-mail form a number of ISP mailboxes and re-deliver them to local mailboxes via sendmail and procmail. You can simplify things and have fetchmail use procmail directly.
The configuration can be as simple or complex as you want: from "dump everything in one, big file" to filing by subject, sender etc. or filter them through SpamAssassin. You can probably choose between "mbox" (all in one file) and "maildir" (one file per message) depending on your Linux, either of which are "plain text" files.
The mail-processing application "formail" also comes in handy for post-processing headers and attachments as they are often just "encoded binary" rather than text. Look for MIME processors from your Linux distribution.
There are other applications out there that do the same kind of thing but the ones I use are: fetchmail, procmail and formail, plus sendmail and SpamAssassin.
If you need to view messages or attachments on a Windows (or any other) box, set up an IMAP server such as UW-IMAP or dovecot that can read the plain "archive" files directly, even directly from CD, and serve them over the network.