I just noticed that some of the links on the main navigation bar on http://jogamp.org/jogl/doc/deployment/JOGL-DEPLOYMENT.html
(and possibly some other pages) point to the wrong places, eg http://jogamp.org/jogl/forum.html
rather than http://jogamp.org/forum.html
, similar for blog links from that page.
Also, you might think about adding a little padding to images (in particular on the jogl showcase)... and I notice that chrome complains about 'unmatched tags' on that page.
from frame with URL http://jogamp.762907.n3.nabble.com/;cid=xxx
. Domains, protocols and ports must match."). Still, seems to be basically working fine. I guess you didn't do anything particularly unusual in embedding Nabble, so maybe it's their problem.
So, nothing show stopping, should all be easy enough to address when anyone has a moment.
Now, having told you what you should do with your site, perhaps I should address some of the problems pointed out by a client of mine on a site I made... :)