Draw an arrow between two divs

You might consider SVG.

In particular, you can use a line with a marker-end shaped with an arrow-path.

Be sure to set orient=auto so the arrowhead will be rotated to match the slope of the line.

Since SVG is a DOM element, you can control the start/end position of the line in javascript.

Here is code and a Fiddle: http://jsfiddle.net/m1erickson/9aCsJ/

<svg width="300" height="100">

    <defs>
        <marker id="arrow" markerWidth="13" markerHeight="13" refx="2" refy="6" orient="auto">
            <path d="M2,2 L2,11 L10,6 L2,2" style="fill:red;" />
        </marker>
    </defs>

    <path d="M30,150 L100,50"
          style="stroke:red; stroke-width: 1.25px; fill: none;
                 marker-end: url(#arrow);"
    />

</svg>