PowerShell port of Don Melton's encode.sh script (https://gist.github.com/donmelton/5734177) to encode video files with HandbrakeCLI. Some things like subtitle support weren't migrated as I don't care for them to be burned in and the Apple TV doesn't support them otherwise. Don's settings are kept intact, with the exception of upping the bitrate…

encode.ps1

<#
	I added the optional decomb PowerShell parameter than activates "--decomb" in Handbrake.
	I was running into interlace issues encoding an animated TV show - Sealab 2021. I don't
	think you will need it unless you're enoding similar content. For everything else I
	leave it off ($false) by default.

	Improved the funcationality of the script to take either a single MKV file or a folder
	of MKV files.

	Usage:
		encode.ps1 [source file]
		encode.ps1 [source directory] -decomb:$true
#>

Param(
	[Parameter(Mandatory = $true, HelpMessage="Please specify an MKV source file or directory.")]
	[string]$source,
	[switch]$decomb
)

[string]$handbrake = "C:\Program Files\HandBrake\HandBrakeCLI.exe"
[string]$mediainfo = "C:\Program Files\MediaInfo\MediaInfo.exe"

$script:handbrake_options = @("--markers", "--large-file", "--encoder", "x264", "--encopts", "vbv-maxrate=25000:vbv-bufsize=31250:ratetol=inf", "--crop", "0:0:0:0", "--strict-anamorphic")

if ($decomb) {
	$script:handbrake_options += "--decomb"
}

function Encode-File {
	Param(
		[Parameter(Mandatory = $true)]
		[string]$source_file
	)

	[string]$output_file = [io.path]::ChangeExtension($source_file, '.mp4')

	[int]$width = & $mediainfo --Inform="Video;%Width%" $source_file
	[int]$height = & $mediainfo --Inform="Video;%Height%" $source_file

	if (($width -gt 1280) -or ($height -gt 720)) {
		$max_bitrate = "6500"
	} elseif (($width -gt 720) -or ($height -gt 576)) {
		$max_bitrate = "4000"
	} else {
		$max_bitrate = "2200"
	}

	[int]$min_bitrate = $max_bitrate / 2

	[decimal]$bitrate = & $mediainfo --Inform="Video;%BitRate%" $source_file

	if (! $bitrate) {
		$bitrate = & $mediainfo --Inform="General;%OverallBitRate%" $source_file
		$bitrate = $bitrate / 10 * 9
	}

	if ($bitrate) {
		$bitrate = [math]::floor($bitrate / 5 * 4 / 100000) * 100

		if ($bitrate -gt $max_bitrate) {
			$bitrate = $max_bitrate
		} elseif ($bitrate -lt $min_bitrate) {
			$bitrate = $min_bitrate
		}
	} else { 
		$bitrate = $min_bitrate
	}

	$script:handbrake_options += "--vb", $bitrate

	[decimal]$frame_rate = & $mediainfo --Inform="Video;%FrameRate_Original%" $source_file

	if (! $frame_rate) { $frame_rate = & $mediainfo --Inform="Video;%FrameRate%" $source_file }

	if ($frame_rate -eq 29.970) {
		$script:handbrake_options += "--rate", 23.976, "--detelecine"
	} else {
		$script:handbrake_options += "--rate", 30, "--pfr"
	}

	[int]$channels =  (& $mediainfo --Inform="Audio;%Channels%" $source_file) -replace "[^0-9].*"

	if ($channels -gt 2) {
		$script:handbrake_options += "--aencoder", "faac,copy:ac3"
	} elseif (((& $mediainfo --Inform="General;%Audio_Format_List%" $source_file) -replace " /.*") -eq "AAC") {
		$script:handbrake_options += "--aencoder", "copy:aac"
	}

	& $handbrake $script:handbrake_options --input $source_file --output $output_file
}

if (Test-Path $source -PathType Container) {
	$files = (Get-ChildItem "$source\*" -include *.mkv)

	if ($files.length -ge 1) {
		ForEach ($file in $files) {
			[string]$mp4file = [io.path]::ChangeExtension($file, ".mp4")
			Write-Host $mp4file
			
			if (!(Test-Path $mp4file)) {
				Write-Host "`n*******************************************************************************"
				Write-Host "Encoding $file" -foreground green
				Write-Host "*******************************************************************************`n"
				Encode-File $file
			} else {
				Write-Host "$mp4file already exists"
			}
		}
	} else {
		Write-Host "`n*******************************************************************************"
		Write-Host "No files are available to encode" -foreground yellow
		Write-Host "*******************************************************************************`n"
	}
} else {
	Encode-File $source
}

I'm still learning PowerShell, so if you see an issue or a better method of doing something, just let me know. I have tried implementing file logging, but PowerShell seems to have an issue with capturing screen output and file output simultaneously. So I'll be looking at file logging in a more granular approach.