Can't have more than 1 item with the same ID, they're not very unique if you do. Change your HTML to:
<ul> <!-- Main Navigation -->
<li ><a class="nav-button" href="welcome/about">ABOUT</a></li>
<li ><a class="nav-button" href="search-listings">SEARCH LISTINGS</a></li>
<li ><a class="nav-button" href="featured">FEATURED</a></li>
<li ><a class="nav-button" href="sell-your-home">SELL YOUR HOME</a></li>
<li ><a class="nav-button" href="welcome/press">PRESS</a></li>
<li ><a class="nav-button" href="welcome/contact">CONTACT</a></li>
</ul>
And the JS:
$( document ).ready(function() {
$(".nav-button").hover(
function(){
console.log('done');
});
});
Here's a fiddle demonstrating it: http://jsfiddle.net/UqyHD/