Although it's handy to be able to flag an important e-mail message in Mail, there is a more eye-catching method. Click to select a message, then open the Colors window by pressing Command-Shift-C. Choose your preferred color, and it will be applied to the message's background in your inbox or in a folder.
[kirkmc adds: Interesting; I see this hasn't been hinted before. In Lion, you have to actually drag the color from the top section of the window - that shows the selected color in a rectangle - onto a message. In Mountain Lion, just click on a color.
This sets the color of the background of a message; if there were a way to set the color of the text of a message, that would be interesting. I use the latter in a number of Mail rules to make specific senders and accounts stand out, and you can set the background color of messages in rules as well.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20120909044052859