Iterate Through All Site Collections Within a Web Application to Change The Site Collection Administrator

If you have many Site Collections in a single web application and you want to set or change the Primary or Secondary Site Collection Administrator without going through each and every one in Central Administration, below is the script you can save as a .ps1 file and run in Powershell.  This script uses (-SecondaryOwnerAlias) to set the Secondary Site Collection Administrator. Change it to (-OwnerAlias) at line 19 to set the primary site collection admin.

## Input Parameters ##
[CmdletBinding()]
Param(
[string]$WebAppUrl=(Read-Host "Please enter a Web Application URL (Example: http://intranet)"),
[string]$Account=(Read-Host "Please enter an account (Example: DOMAIN\Administrator)")
)
## Add SharePoint Snap-in ##
Add-PSSnapin Microsoft.SharePoint.PowerShell -erroraction SilentlyContinue
### No need to modify these ###
$WebApp = Get-SPWebApplication $WebAppUrl
$AllSites = $WebApp | Get-SPSite -Limit ALL

##The Script - no need to modify this section ##
## Start SP Assignment for proper disposal of variables and objects ##
Write-Host "Starting SP Assignment..." -ForegroundColor Green
Start-SPAssignment -Global
## Use a ForEach-Object loop and Set-SPSiteAdministration to set an entire web application ##
Write-Host "Adding $Account to $WebAppUrl as a Site Collection Administrator..." -ForegroundColor Yellow
$AllSites | ForEach-Object { Set-SPSite -SecondaryOwnerAlias $Account -Identity $_.url }
## End SP Assignment for proper disposal of variables and objects ##
Write-Host "Disposing of SP Objects.." -ForegroundColor Green
Stop-SPAssignment -Global
## Tell us it's done ##
Write-Host "Finished!" -ForegroundColor Green