上記の例でblobを処理できなかったため、upload.phpの内容を正確に知りたいと思いました。だからここに行きます:
(Chrome 28.0.1500.95でのみテスト済み)
// javascript function that uploads a blob to upload.php
function uploadBlob(){
    // create a blob here for testing
    var blob = new Blob(["i am a blob"]);
    //var blob = yourAudioBlobCapturedFromWebAudioAPI;// for example   
    var reader = new FileReader();
    // this function is triggered once a call to readAsDataURL returns
    reader.onload = function(event){
        var fd = new FormData();
        fd.append('fname', 'test.txt');
        fd.append('data', event.target.result);
        $.ajax({
            type: 'POST',
            url: 'upload.php',
            data: fd,
            processData: false,
            contentType: false
        }).done(function(data) {
            // print the output from the upload.php script
            console.log(data);
        });
    };      
    // trigger the read from the reader...
    reader.readAsDataURL(blob);
}
upload.phpの内容:
<?
// pull the raw binary data from the POST array
$data = substr($_POST['data'], strpos($_POST['data'], ",") + 1);
// decode it
$decodedData = base64_decode($data);
// print out the raw data, 
echo ($decodedData);
$filename = "test.txt";
// write the data out to the file
$fp = fopen($filename, 'wb');
fwrite($fp, $decodedData);
fclose($fp);
?>