How can I make box-shadow appear above a div?

It's #top and its box-shadow that you want to appear on top, so give that position: relative instead of giving position: relative to #middle. There's no need for z-index: 0.

http://jsfiddle.net/thirtydot/QqME6/1/

#top {
    width: 100%;
    height: 100px;
    box-shadow: 3px 3px 3px #333;
    background-color: blue;
    
    position: relative;
}

#middle {
    width: 100%;
    height: 200px;
    background-color: orange;
}

#innerMiddle {
    width: 200px;
    height: 200px;
    margin: 0 auto;
    background-color: green;
}
<div id="top">
</div>

<div id="middle">
    <div id="innerMiddle">
    </div>
</div>

Change your CSS to: 

#top {
    width: 100%;
    height: 100px;
    box-shadow: 3px 3px 3px #333;
    background-color: blue;
    position:relative;
    z-index:1;
}

#middle {
    width: 100%;
    height: 200px;
    z-index: 0;
    position: relative;
    background-color: orange;
}
<div id="top">
</div>

<div id="middle">
    <div id="innerMiddle">
    </div>
</div>

Tags:

Html

Css

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