Is there a way for me to add Yahoo mail to the Mail app in such a way that when it syncs my email, the emails won't be marked as "read" on the online version of my Yahoo! mail?

I don't believe so. Yahoo (as far as I can tell) only offers POP e-mail, not IMAP. And however they have POP set up, it's configured to mark e-mail as read on the web interface when a client downloads it.

Basically all Mail is doing is asking for the messages. Yahoo's servers are then also marking them read.

Something Tom implied, but didn't say explicity is:

If Yahoo offered an IMAP interface instead of a POP interface, then it would Just Work The Way You Want It To.

Gmail will do IMAP. My iPhone mail and my Gmail are perfectly synched at all times. Just sayin'.

The odd thing is that Yahoo does offer IMAP e-mail, but only for specific devices/setups. The iPhone is one of them, and the Zimbra software can use it as well. The server is imap.mail.yahoo.com, but it rejects attempts to use it unless you have an approved device or program.

So burdell1 is talking about the Mail app on a macintosh computer, and that's one of the specific configurations where Yahoo rejects the imap connection? Wow, that's just painful.

How does it know? There's no client identification in IMAP. Does the Yahoo IMAP server require a nonstandard protocol change?

Actually, I think the IMAP server is imap.n.mail.yahoo.com. I don't have a Yahoo email address, so I can't test it, but it's worth a shot.

imap.n.mail.yahoo.com and imap.mail.yahoo.com are the same server based on what I'm seeing them resolve to. Also, RFC 2971 adds "IMAP ID", a way of identifying clients. It's possible Yahoo enforces this RFC on their server.

I did try setting up my Yahoo account on my iPhone, and it works fine, but no luck in Mail. Using default settings, it tries pop and asks me to subscribe to Yahoo Mail Plus. Using IMAP, mail reports back that the server is not responding. Didn't matter if I had SSL on or not, nor trying ports 143 and 993. Telnetting to the server on 143 does result in a normal looking IMAP response, so they are doing something to block clients.