I like to see the new mail popup when I get emails, but not for all emails. Only my boss is important enough to distract me from whatever I'm working on. So…
how do I display the alert from my boss, but not from anyone else?
Turn off Desktop New Mail Alerts
First I'll turn off desktop alerts completely.
Tools » Options » Preferences tab
Click [E-mail Options...], then [Advanced E-mail Options...]
Uncheck "Display a New Mail Desktop Alert (default Inbox only)"

Set up New Mail Rule
Then I'll set up a rule to display the desktop alert from my boss only.
Tools » Rules and Alerts…
Create a new blank rule to check incoming messages. Select "from people or distribution list" and select the names from your Contacts list (or GAL) that you want the desktop alert for. In the Action(s) section, find "display a Desktop Alert". The final result should look like:

Save and exit the Rules Wizard. Now you'll only see the new mail popups when the contacts you selected send you an email!
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