Thanks for pointing out the javascript degration and the spotlight coded not being flash.

The spotlight (carousel) items on the front page are coded in javascript rather than relying on Flash. Personally, it frustrates me so much when I see simple sliders like that implemented in Flash, when you could achieve basically the same effect by using javascript, making it more usable and accessible for multiple reasons.
Many of the javascript-reliant features on the site are coded to degrade gracefully when a user visits with javascript disabled (which can also be important if a minor bug shows up somewhere along the way in your javascript code that suddenly renders all of your JS inoperable).
Although it’s far from perfect, you can definitely tell that the developer is trying to make the code efficient and valid (which is far from easy when using Joomla or Mambo as the CMS), but just hasn’t gotten things where they need to be, yet.

Overall, this site still has a long way to go, but you can tell that the developer is trying to make the best of a bad situation.

My quick suggestions for some (should be) simple fixes:

Render the “Quicklinks” menu with javascript, rather than having it hardcoded into the template. Since it doesn’t expand without javascript enabled, there’s no point in having the little tag at the top of the screen when javascript is disabled.
Fix the main promotional area pagination/navigation when javascript is disabled:

Either render those pagination links with javascript so that they don’t show up when JS is disabled or
Create them as real links with query strings that will manually load the new promotional items when javascript is disabled

Fix the “description” and “keywords” meta tags for the site. Descriptions and keywords are more harmful when repeated than they are when left blank.
Move javascript calls to the foot (just above the closing </body> tag) rather than placing them in the head of the document.
Consider switching to jQuery if possible, as it offers a great deal more functionality and lets you remove a lot of your inline javascript (such as the onmouseover, onclick, etc. event handlers) out of the body of your page and place them in external JS files. If you can’t switch to jQuery (I know it can be difficult to make the transition from MooTools to jQuery, as I recently made that change on our site, and still haven’t got some of our image carousels working as well as they did with MooTools), at least consider using the Google Hosted MooTools to save a little on your bandwidth and to add to the possibility that your visitors will already have it cached in their browsers
Constantly run your pages through various validators. Make sure your HTML code and your CSS validate (or, that you at least have really good reasons why the don’t validate) and check various pages on the Cynthia Says accessibility validator from time to time.

Just want to point out one error in your analysis. You indicate they should remove the Google verification code to save bandwidth however this is inaccurate. The code must remain as Google will periodically re-verify the site. http://www.google.com/support/webmasters/bin/answer.py?answer=35659