Делается так
<script type="text/javascript">
function runProgram(appName){
alert(appName);
document.getElementById('programRunFrame').src='file://'+appName;
}
</script>
<iframe id="programRunFrame" style="display:none;"></iframe>
....
<input type="file" id="program_selector" />
<button onclick="runProgram(document.getElementById('program_selector').value);">Запустить</button>
....