You've got a few things going on there. One, why a class? Do you actually have multiple of these on the page? The CSS suggests you can't. If not you should use an ID - it's faster to select both in CSS and jQuery:
<div id=bottomMenu>You read it all.</div>
Second you've got a few crazy things going on in that CSS - in particular the z-index is supposed to just be a number, not measured in pixels. It specifies what layer this tag is on, where each higher number is closer to the user (or put another way, on top of/occluding tags with lower z-indexes).
The animation you're trying to do is basically .fadeIn(), so just set the div to display: none; initially and use .fadeIn() to animate it:
$('#bottomMenu').fadeIn(2000);
.fadeIn() works by first doing display: (whatever the proper display property is for the tag), opacity: 0, then gradually ratcheting up the opacity.
Full working example:
http://jsfiddle.net/b9chris/sMyfT/
CSS:
#bottomMenu {
display: none;
position: fixed;
left: 0; bottom: 0;
width: 100%; height: 60px;
border-top: 1px solid #000;
background: #fff;
z-index: 1;
}
JS:
var $win = $(window);
function checkScroll() {
if ($win.scrollTop() > 100) {
$win.off('scroll', checkScroll);
$('#bottomMenu').fadeIn(2000);
}
}
$win.scroll(checkScroll);