Rename Web Application and Alternate Access Mapping Collection

$wa = Get-SPWebApplication | where {$_.Name -match "localhost - 80"}
$wa.Name = "My Web App"
$wa.Update()
$aamc = $wa.AlternateUrls
$aamc.Name = "My Web App"
$aamc.Update()

Resources:
http://www.topsharepoint.com/rename-web-application-in-sharepoint-2010