Import Audio Markers or Cues to Audition CS5.5
And as I spent the last two days hunting down a solution, I'll share it with you right away:

tl;dr: Use this cross platform &amp; open source tool by the US Government (ya, really) to stick XMP Metadata in the WAV File.
http://bwfmetaedit.sourceforge.net/

WAV Files support the "cue " chunk, and this chunk is written by Audition, but I couldn't make it read from this chunk, and related chunks containing the cue names.

But Audition also writes the XMP Metadata, including a somewhat redundant copy of the Cue chunk. And it will also read it back.

So, by generating an XMP file containing the cue information, and sticking it in the XMP chunk of a WAV file, you can import that data to Audition.

For example:

&lt;?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?&gt;
&lt;x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Adobe XMP Core 5.2-c003 61.141987, 2011/02/22-12:03:51        "&gt;
   &lt;rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"&gt;
      &lt;rdf:Description rdf:about=""
            xmlns:xmpDM="http://ns.adobe.com/xmp/1.0/DynamicMedia/"&gt;
         &lt;xmpDM:Tracks&gt;
            &lt;rdf:Bag&gt;
               &lt;rdf:li rdf:parseType="Resource"&gt;
                  &lt;xmpDM:trackName&gt;CuePoint Markers&lt;/xmpDM:trackName&gt;
                  &lt;xmpDM:trackType&gt;Cue&lt;/xmpDM:trackType&gt;
                  &lt;xmpDM:frameRate&gt;f254016000000&lt;/xmpDM:frameRate&gt;
                  &lt;xmpDM:markers&gt;
                     &lt;rdf:Seq&gt;
                        &lt;rdf:li rdf:parseType="Resource"&gt;
                           &lt;xmpDM:startTime&gt;18645250f44100&lt;/xmpDM:startTime&gt;
                           &lt;xmpDM:name&gt;Marker 01&lt;/xmpDM:name&gt;
                        &lt;/rdf:li&gt;
                        &lt;rdf:li rdf:parseType="Resource"&gt;
                           &lt;xmpDM:startTime&gt;69088263f44100&lt;/xmpDM:startTime&gt;
                           &lt;xmpDM:name&gt;Marker 02&lt;/xmpDM:name&gt;
                        &lt;/rdf:li&gt;
                     &lt;/rdf:Seq&gt;
                  &lt;/xmpDM:markers&gt;
               &lt;/rdf:li&gt;
            &lt;/rdf:Bag&gt;
         &lt;/xmpDM:Tracks&gt;
      &lt;/rdf:Description&gt;
      &lt;rdf:Description rdf:about=""
            xmlns:dc="http://purl.org/dc/elements/1.1/"&gt;
         &lt;dc:format&gt;audio/x-wav&lt;/dc:format&gt;
      &lt;/rdf:Description&gt;
   &lt;/rdf:RDF&gt;
&lt;/x:xmpmeta&gt;


The format should be self explanatory.

If you want to write your own tool to automate this, follow the XMP specs from Adobe concerning WAV files and the XMP chunk, which, ironically is named backwards:


  The XMP in […] WAV is in a chunk with the ID "_PMX", encoded as UTF-8.
  Note that the ID is backwards, due to a bug in the initial
  implementation concerning processor byte order.


Here's an iOS App that will generate Audition-compatible XMP files: 
http://itunes.apple.com/us/app/xmp-marker/id525322095?ls=1&amp;mt=8