If I had to choose one, it would be the support for
message: URIs in Mail.app.
It allows you to:
- send a link to a message to a friend: if he also got that message but "lost" it somehow, he can just click and let Mail.app find it;
- you can store URIs to important messages on any other Mac application, and in a Cocoa app, just right-click to jump to it;
- it allows interesting integration between web applications and your local mail client: it should be pretty simple for someone to write a "Open in Mail.app"-scriptlet that works inside GMail or others webmails.
I used to have MailTags installed just for this, but now, it just works out of the box.
I noticed this feature before but Gruber wrote a nice article about it that triggered my memory.