Mail.app 3 has started a love/hate relationship with me. Some of the new features are just fantastic, and, it's been pretty stable. However, there are definitely some annoyances. I've already mentioned the syncing thing, and now, I have another. Mail.app doesn't truly "go offline" when you select "Take All Accounts Offline." It will still try to contact SMTP servers. So, if you're offline, compose a message and queue it for sending, that's it - it's "gone." You won't have an outbox (because you're "offline") but as soon as you have a network connection, zip! Off it goes.
Yes, I've sent the requisite feedback/bug reports.