This is a real long shot but wondering if anyone came up with a way to do this. We have plenty of email notifications to mailboxes and cell phone but what about notifying someone with a Lync popup message too. Since they are both MS products, I thought maybe there was some way to do this?

There is no built-in integration between Service Manager and Lync. You may want to take a look at Derdack. They are the only ones I know that have Lync notification capabilities that integrate with Service Manager. 

Emergency and Mass Notifications for Microsoft Lync