Well, first of all, as a Linux User, please change the Mac instructions on the software page to indicate that Linux Users need to also perform the same cntl-click that mac Users do in order to use the package. I had trouble figuring it out.
secondly, try placing the Link (nice 3d image) up in the header, (maybe above the Search Box), so that the software is consistently available on each and every page.
thirdly, reduce the height of the header so that the prime information is moved "above the fold" on the Index page. Gives the viewer some information really quickly and as nice as the site is, It takes too long to figure out where all the good stuff is. Example, the left hand sidebar takes too much attention away from the purpose for the site. maybe reduce its width and let the centre content stand out more or use a horizontal nav bar layout. See also the below suggestion to create more value on the first page impression.
next, drop the flash down below the "blurb" or into the right sidebar. (Might want to look at using a thickbox for the video presentation.)
And lastly, lose the Google ads. They are distracting from the page's purpose. Show them on subsequent pages, but not the main page.
Hope that helps and good luck with the site.