I found a script using Technet and Google.
$outlook = New-Object -comObject Outlook.Application
$olJunk = $outlook.Session.GetDefaultFolder(23)
$($olJunk.Items) | %{$_.Delete()}
It turns out it does actually empty the junk mail folder. I guess each default folder is assigned a numerical value.
What I'm looking for is a way to actually backup the folder contents before the delete. In a sense doing the equivalent of a pst backup using powershell. I'm hoping I can get powershell to select the folder and mimic the action of a Import/Export to .pst.
I don't even know if this is possible, anyone have any ideas? Thanks...