> The links in the javascript are not recognized by
> HTTrack.  Is there something I can do to the
> Javascript to make the links work?  Is there
> something I can do with HTTrack to mirror these
> links?
The best solution is to ensure that the links are _real_ links ; that is,
links you can use even with very "raw" browsers, such as lynx. To be simple:
javascript should be a "cosmetic feature", not a mandatory element to use the
pages. The other hint is to use very simple javascript, with URL embedded in
code.

Example:
(a href="page42.php" onClick="return someaction('section42.php');")This is a
friendly link(/a)

In this example, let say that "someaction()" is a function that will
dynamically load a submenu with some nice dynamic ajax-thing, and page42.php a
regular html page for old-fashioned browsers.

That way, you will:
(1) be compatible with very old browsers, text-mode browsers, and browsers
designed for disabled (blind/visually impaired) people
(2) be easily crawlable by search engines
(3) be crawlable by httrack :)