Email flags in Mac Mail

This AppleScript will set the flag of the selected message to red:

tell application "Mail"
	set msg to item 1 of (get selection)
	tell msg
		set flag index to 0
	end tell
end tell

Change 0 to 1 or 2 or 3 or 4 or 5 or 6 for different colors.
Change 0 to -1 to remove the flag

Also check out this post by Chris.