I've been pretty happy with Dovecot's mdbox format. This stores multiple emails per file and multiple files per mailbox which alleviates the problem of ending u

I've been pretty happy with Dovecot's mdbox format. This stores multiple emails per file and multiple files per mailbox which alleviates the problem of ending up with millions of files in one directory on filesystems which aren't tuned for this. Metadata is stored (only) in a separate index file which at first feels a bit "brittle", but this also alleviates a lot of the downsides of "indexed Maildir" type solutions (no more need to check for consistency between index and filesystem etc). Breaking with the idea that the entire email is stored in a single file (whether with other emails as with mbox or on its own as with Maildir etc) then also lets you do things like deduplicating attachments between emails (this was my primary motivation for exploring it). The main downside for me is that you can only really access the mailbox using dovecot/IMAP as tools like mutt don't support it.