This post assumes that you know about Flags and used them already (if not look in the menu “Message/Flag/…”.
Add a keyboard shortcut
The next interesting step is to attach a keyboard shortcut to this flag. Open “System Preferences” and go to “Keyboard”. There select the “Keyboard Shortcuts” tab and under “Application Shortcuts you add a new entry (by clicking on the “+” symbol).
Edit the entry. Make sure you use the same name you gave the flag. Here it’s probably getting interesting if you chose a name that already exists somewhere else in the Mail.app menu… (did not try that).
Finally the tagging / labeling feature I used so much in Mozilla Thunderbird is available in Mail.app as well