Why can't you use absolute positioning? Vertical-align does not work (except for tables). Make your container's position: relative. Then absolutely position the internal divs using bottom: 0; Should work like a charm.
EDIT By zoidberg (i will update the answer instead)
<div style="position:relative; border: 1px solid red;width: 40px; height: 40px;">
<div style="border:1px solid green;position: absolute; bottom: 0; left: 0; width: 20px; height: 20px;"></div>
<div style="border:1px solid blue;position: absolute; bottom: 0; left: 20px; width: 20px height: 20px;"></div>
</div>