You want to display the option dates in the format "2006, June, 20", and to pass the selected value in the format "2006-06-20". Is that correct? If so, then:
for ($d = 0; $d <= 90; $d++) {
$ts_date = strtotime('-' . $d . ' days');
$value_date = date('Y-m-d', $ts_date);
$display_date = date('Y, F, j', $ts_date);
echo '<option value="' . $value_date . '">' . $display_date . '</option>';
}
I know you've been introduced to strtotime() at least a couple of times before. When you learn to use it your date manipulation problems will be less frequent.