I finally had time to sit down and figure out how to set the from and reply-to fields for mail messages and associate internal messages to sender user accounts for sending methods like privatemsg.
There have been quite a few configuration options added as well. Hutch got the ball rolling with a few label configurations and it just snowballed from there. I couldn't help myself, and I feel that the user interface is now very flexible:
Issue #1391488 by acrazyanimal: Added configurable defaults, collapsible form wrapper, and handling of token replacements.
Issue #1243308 by hutch: Added configurable labels and wrapped reply form in a collapsible fieldset.
