Suggest a checkbox be placed in each message to allow selection/deselection, much like you would find in any webmail page such as Yahoo! or Hotmail.

At the top & bottom of the page have "Select All" "Hide Selected" "Print Selected" and "Email Selected" buttons to allow only specified messages to be printed, emailed to someone or removed from view.

Perhaps the "Print Selected" button is not necessary at all. Once specific messages are (optionally) selectively removed from view with the "hide" button, the browser's "Print" button would be all that is really needed for printing operations.

Selections should apply to the entire thread rather than just those on the current viewable page.

This capability would be a vast improvement to replace the current "print thread" button which is really rather useless if the thread is very long.