If you want Modernizr to download and execute as soon as possible to prevent a FOUC, put it in the <head>
From their installation guide:
Drop the script tags in the
<head>of
your HTML. For best performance, you
should have them follow after your
stylesheet references. The reason we
recommend placing Modernizr in the
head is two-fold: the HTML5 Shiv (that
enables HTML5 elements in IE) must
execute before the<body>, and if
you’re using any of the CSS classes
that Modernizr adds, you’ll want to
prevent a FOUC.