Mail 1.3.9 Suggestions

Allow selection of multiple emails per contact in the Address Book email selection pane
As is, you can only select one email per person, even when holding down the apple key or the shift key. This is useful if you're not sure which email the contact will see first or if you're not sure which email is current. The current pain in the butt workaround is to add the email and then go back and click again to add the second.

Apply rules to sent emails
As is, if you want to have rules applied to sent emails, you have to go to the sent folder, select all, and select apply rules from the message menu. This should be automatic or else it should be a preference: "Apply rules to sent emails."

Make it possible to hide Out / Drafts / Sent / Trash / Junk
These do not always need to be in view. Menu items in the view menu or a submenu thereof would do the trick nicely.

Move Trash and Junk to the bottom of the drawer
They should be listed at the bottom below user-created folders so that more important things can have higher prominence.

Organize rules with nested folders
As is, you just end up having a very long awkward list if you use a lot of rules. Folders would make things a heckuva lot easier to deal with. The order of rule implementation wouldn't change... you would just open the folder and take things in the order they are in inside before going on to the next item.

Make a tool bar button for Apply Rules
This is one of the few things I have to dig through the menu for again and again.

Ability to add and remove emails to and from threads
Right now emails with exactly the same subject may be threaded together even when they are not related. For instance, "Re: hey" is a common email subject among my friends and they often end up bunched together even when totally unrelated.

This could be implemented in a very simple way. If you want to thread one email with another, drag the email to be threaded to the other email. If that email is already in a thread, the added email will become part of that thread. If you want to thread two threads together, drag the header of the thread to another email in the other thread. If you want to remove an email from a thread, simply drag it out of the tread onto another part of the mail window. You should be able to use select and command to select multiple emails for the same treatment.

Add an email to an existing contact in Address Book
As is, the only thing you can do with emails and Address Book is "Add to Address Book," which creates a new contact in the address book. However, often an email is received from someone already in your address book and no new entry is needed. Thus an "Add Email to Existing Contact" function should be added to the email drop-down menu. This function should open up the Address Book window to select the person you're looking for, the the "To:" and "CC:" buttons replaced by "Add". If the email is sent with a name, that name should be automatically entered in to the Address Book pane search field, which is where the cursor should automatically go, highlighting the entire field so you can readily type in it.