Mail’s toolbar looks something like this (click it to zoom in):
Turns out you can add a skinny toolbar underneath the main toolbar. Actually, it’s not a toolbar: it’s the Favorites Bar” (shown outlined in red below). Looks like this (click this one to zoom in too):
Clicking on a Favorite takes you there right away, as if you clicked that Mailbox in Mail’s left-hand pane. You can drag and drop a mail message into one of the Favorites and in it goes, same as if you dragged it to the corresponding Folder (mailbox) in the list on the left, making for some quick and easy filing. The advantage of dragging an email to the Favorites bar is the list at the left is alphabetical, so there can be some scrolling involved, while the items in the Favorites bar can be in any order you’d like (so no scrolling required). Put folders (mailboxes) that you would have to scroll down to find into the Favorites Bar– they’ll still be in the list of mailboxes at the left, but now they’ll also be accessible at the top, without scrolling.
Put mailboxes into Mail’s Favorites bar by dragging from the list at the left to the Favorites bar. Take things out of the Favorites bar by dragging them off. Couldn’t be easier.
I find the Favorites Bar very handy and you will too. Try it.
Note: this works in older versions of Mac OS. It is not “new in Yosemite.”