No lo he podido probar, y aún así las funcionalidades están un poco limitadas. Pero se puede usar Skype mediante PHP, aunque necesitaremos:

• PHP5
• Skype4COM (documentación)

Un ejemplo sería el siguiente:

<?php
// Event sink:
class _ISkypeEvents {
function AttachmentStatus($status) {
echo ">Attachment status $status\n";
}
function CallStatus($call, $status) {
echo ">Call $call->id status $status\n";
}
}
// Create a Skype4COM object:
$skype = new COM("Skype4COM.Skype");
// Create a sink object:
$sink =& new _ISkypeEvents ();
$sink->convert = $skype->convert();
// Connect to the sink:
com_event_sink($skype, $sink, "_ISkypeEvents");
// Create a conversion object:
$convert = $skype->convert;
$convert->language = "en";
// Start the Skype client, minimized and with no splash screen:
if (!$skype->client()->isRunning()) {
$skype->client()->start(true, true);
}
// If the user status is not "online", change user status to "online":
if ($skype->currentUserStatus() == $convert->textToUserStatus("OFFLINE")) {
$skype->changeUserStatus($convert->textToUserStatus("ONLINE"));
}
// Create a user object
$user = $skype->user("echo123");
echo "User " . $user->handle . " online status is " . $convert->onlineStatusToText($user->onlineStatus) . "\n";
// Place a call
$call = $skype->PlaceCall($user->handle);
// Wait for the call to be "in progress" and report an error if:
while ($call->status <> $convert->textToCallStatus("INPROGRESS")) {
if ($call->status == $convert->textToCallStatus("FAILED") ||
$call->status == $convert->textToCallStatus("REFUSED") ||
$call->status == $convert->textToCallStatus("CANCELLED") ||
$call->status == $convert->textToCallStatus("FINISHED") ||
$call->status == $convert->textToCallStatus("BUSY"))
die ("Call status " . $convert->callStatusToText($call->status));
else
com_message_pump (500);
}
// Send dtmf tones:
com_message_pump (10000);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "0";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "1";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "2";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "3";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "4";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "5";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "6";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "7";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "8";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "9";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "#";
com_message_pump (500);
if ($call->status == $convert->textToCallStatus("INPROGRESS")) $call->dtmf = "*";
// Finish the call:
if ($call->status <> $convert->textToCallStatus("FINISHED")) $call->finish();
//Sleep:
com_message_pump (1000);
?>

Example Call.php