If you are finding mail sometimes not appearing in your Mail inbox after upgrading to Snow Leopard, but then it appears again once you restart Mail, try shutting off the ‘Use IDLE command’ option in account settings. (Its at the bottom of the advanced tab).

After upgrading to Snow Leopard on my Mac, I noticed this was happening with email in my Dreamhost IMAP account.

I’ve been running with the ‘IDLE’ option turned off for a day, and it seems to be working correctly again.