$site = Get-SPSite http://mysite
$web = $site.OpenWeb()
$list = $web.Lists["List Name"]
$wp = $list.RootFolder.Name + "/Forms/AllItems.aspx"
$wpManager = $website.GetLimitedWebPartManager($wp, [System.Web.UI.WebControls.WebParts.PersonalizationScope]::Shared)
$webpart = $wpManager.WebParts[0]
$webpart.JSLink = "~SiteCollection/_catalogs/masterpage/myScript.js"
$wpManager.SaveChanges($webpart)

Add-PSSnapin Microsoft.SharePoint.PowerShell -ErrorAction SilentlyContinue
$web = Get-SPWeb http://sharepointsite
$list = $web.Lists["TestJSLink"]
$wp = $list.RootFolder.Name + "/Forms/AllItems.aspx"
$wpManager = $web.GetLimitedWebPartManager($wp, [System.Web.UI.WebControls.WebParts.PersonalizationScope]::Shared)
$webpart = $wpManager.WebParts[0]
$webpart.JSLink = "~layouts/XYZ/JSLink.js"
$wpManager.SaveChanges($webpart)
Write-Output "Done"