http://jsfiddle.net/cnmsc1tm/

This won't work with IE8 or below because of CSS limitations.

function getOffset( el ) {
    var rect = el.getBoundingClientRect();
    return {
        left: rect.left + window.pageXOffset,
        top: rect.top + window.pageYOffset,
        width: rect.width || el.offsetWidth,
        height: rect.height || el.offsetHeight
    };
}

function connect(div1, div2, color, thickness) { // draw a line connecting elements
    var off1 = getOffset(div1);
    var off2 = getOffset(div2);
    // bottom right
    var x1 = off1.left + off1.width;
    var y1 = off1.top + off1.height;
    // top right
    var x2 = off2.left + off2.width;
    var y2 = off2.top;
    // distance
    var length = Math.sqrt(((x2-x1) * (x2-x1)) + ((y2-y1) * (y2-y1)));
    // center
    var cx = ((x1 + x2) / 2) - (length / 2);
    var cy = ((y1 + y2) / 2) - (thickness / 2);
    // angle
    var angle = Math.atan2((y1-y2),(x1-x2))*(180/Math.PI);
    // make hr
    var htmlLine = "<div style='padding:0px; margin:0px; height:" + thickness + "px; background-color:" + color + "; line-height:1px; position:absolute; left:" + cx + "px; top:" + cy + "px; width:" + length + "px; -moz-transform:rotate(" + angle + "deg); -webkit-transform:rotate(" + angle + "deg); -o-transform:rotate(" + angle + "deg); -ms-transform:rotate(" + angle + "deg); transform:rotate(" + angle + "deg);' />";
    //
    // alert(htmlLine);
    document.body.innerHTML += htmlLine;
}

• The Distance Formula
• Finding the Center Of Two Points
• Finding the Angle Between Two Points
• CSS Transform:Rotate
• HTML Element offset[Width|Height|Top|Left] properties

Edit (for others with the same problem):

If you need to, for example, create a line from two corners that are not the top right and bottom right divs, go to this section of the code:

// bottom right
var x1 = off1.left + off1.width;
var y1 = off1.top + off1.height;
// top right
var x2 = off2.left + off2.width;
var y2 = off2.top;

where you see + off1.width and + off1.height, that means that the code is calculating the position of the bottom or the right of the div. Remove the + off1.width or the + off1.height to get the left or the top of the div.

EDIT updated to a more standard getOffset function. If you want to get really anal you'd probably also have to add document.documentElement.client[Left/Top] and walk the offsetParent tree, but I think getBoundingClientRect() and window.page[X/Y]Offset are sufficient for an example like this.