Overall, good job with the design! Much better than the old one at least ;D.
I do agree with Zwei that it looks quite empty on the right side of the top banner. Maybe you can move the rAthena logo there as suggested (or at least some RO-related image or maybe take a screenshot of the community forums, etc), and then add a small rA logo (or resize the one you guys made) in the blue navigation bar (I think it'll look empty there D: on the left side if it's removed completely). Or, you can shift the words to the left if the logo does get moved (though I still prefer a small image in the navigation bar).
Furthermore, the footer links can be edited. The "Home" button can link to the main page or set it as # so the viewer can be scrolled to the top of the page. For the "Contact Us" button, you should link viewers to this page http://rathena.org/board/index.php?app=forums&module=extras§ion=stats&do=leaders if you have no other pages (or the staff page I guess). Lastly, the IRC button can be linked to this page http://rathena.org/board/topic/56196-irc-channel-rules/ =D!
One last thing, I still think the name of the board should be rAthena Board instead of RAthena Board. Same with the first tab of the navigation bar on the forums. Just some suggestions/things that I've noticed. Nothing big that should be rushed upon.
Great way to start off the new year at rAthena with the new website! Nice <3. Keep up the amazing works =D!