user14384: I'm trying to find the best application on windows to do this HD to SD conversion for a video server which requires files to be exactly 720x480/29.97fps MP4 H.264 to function. I can't find any options for leterboxing in Handbrake so I suppose I'll need an alternative.

user1871: You can use ffmpeg, a free command-line tool, to do this:
Without letterboxing, NTSC wide pixel-aspect
ffmpeg -i input.mp4 -vf "scale=720x480,setdar=16/9" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4 

With letterboxing, NTSC 4:3 pixel-aspect
ffmpeg -i input.mp4 -vf "pad=1920:1440:0:180,scale=720x480,setdar=4/3" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4

With letterboxing, square pixels
ffmpeg -i input.mp4 -vf "scale=720x404,pad=720:480:0:38,setsar=1" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4

Read up on sample or pixel aspect ratios, if you're unfamiliar with them. Your requirements make it sound like NTSC-spec files are expected, so try the commands in the order listed.
If your source audio is MP4-ready i.e. of codec AAC or MP3, then you can replace -c:a aac with -c:a copy

14384: <p>I'm trying to find the best application on windows to do this HD to SD conversion for a video server which requires files to be exactly 720x480/29.97fps MP4 H.264 to function. I can't find any options for leterboxing in Handbrake so I suppose I'll need an alternative.</p>
 1871: <p>You can use <a href="http://ffmpeg.org/download.html" rel="nofollow">ffmpeg</a>, a free command-line tool, to do this:</p>

<h3>Without letterboxing, NTSC wide pixel-aspect</h3>

<pre><code>ffmpeg -i input.mp4 -vf "scale=720x480,setdar=16/9" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4 
</code></pre>

<h3>With letterboxing, NTSC 4:3 pixel-aspect</h3>

<pre><code>ffmpeg -i input.mp4 -vf "pad=1920:1440:0:180,scale=720x480,setdar=4/3" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4
</code></pre>

<h3>With letterboxing, square pixels</h3>

<pre><code>ffmpeg -i input.mp4 -vf "scale=720x404,pad=720:480:0:38,setsar=1" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4
</code></pre>

<p>Read up on sample or <a href="https://en.wikipedia.org/wiki/Pixel_aspect_ratio" rel="nofollow">pixel aspect ratios</a>, if you're unfamiliar with them. Your requirements make it sound like NTSC-spec files are expected, so try the commands in the order listed.</p>

<p>If your source audio is MP4-ready i.e. of codec AAC or MP3, then you can replace <code>-c:a aac</code> with <code>-c:a copy</code></p>
