How do you embed an external URL (to a software application) in Drupal with 508 compliance?
I can't find a single reference on Google that says iFrames aren't section 508 compliant...however they will fail compliance if you do not:


  Provide alternative content for IFRAME elements


iFrames can contain nested alternative content, like so:

&lt;iframe src="frame.html"&gt;
  &lt;p&gt;Description of the loaded content&lt;/p&gt; 
&lt;/iframe&gt;


The rationale listed for this is:


  Some browsers do not support the IFRAME element, or do not have the ability to load multiple documents together. It is therefore necessary to provide alternative content for this element even if the IFRAME only loads HTML.


This information came from here, but all of the other links I found on Google said exactly the same thing in one way or another.