Este script php está funcionando muy bien para cambiar los collation de una base de datos. Cambia todo los collation no solo de las tablas sino también de los campos por lo que es muy completo.

<?php

function MysqlError()
{
if (mysql_errno())
{
echo "Mysql Error: " . mysql_error() . "\n";
}
}

$username = "username_de_bd";
$password = "password_de_bd";
$db = "base_de_datos";
$host = "localhost";

$target_charset = "utf8";
$target_collate = "utf8_general_ci";

echo "

";

$conn = mysql_connect($host, $username, $password);
mysql_select_db($db, $conn);

$tabs = array();
$res = mysql_query("SHOW TABLES");
MysqlError();
while (($row = mysql_fetch_row($res)) != null)
{
        $tabs[] = $row[0];
}

// now, fix tables
foreach ($tabs as $tab)
{
        $res = mysql_query("show index from {$tab}");
        MysqlError();
        $indicies = array();

        while (($row = mysql_fetch_array($res)) != null)
        {
                if ($row[2] != "PRIMARY")
                {
                        $indicies[] = array("name" => $row[2], "unique" => !($row[1] == "1"), "col" => $row[4]);
                        mysql_query("ALTER TABLE {$tab} DROP INDEX {$row[2]}");
                        MysqlError();
                        echo "Dropped index {$row[2]}. Unique: {$row[1]}\n";
                }
        }

        $res = mysql_query("DESCRIBE {$tab}");
        MysqlError();
        while (($row = mysql_fetch_array($res)) != null)
        {
                $name = $row[0];
                $type = $row[1];
                $set = false;
                if (preg_match("/^varchar\((\d+)\)$/i", $type, $mat))
                {
                        $size = $mat[1];
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} VARBINARY({$size})");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} VARCHAR({$size}) CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }
                else if (!strcasecmp($type, "CHAR"))
                {
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} BINARY(1)");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} VARCHAR(1) CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }
                else if (!strcasecmp($type, "TINYTEXT"))
                {
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} TINYBLOB");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} TINYTEXT CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }
                else if (!strcasecmp($type, "MEDIUMTEXT"))
                {
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} MEDIUMBLOB");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} MEDIUMTEXT CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }
                else if (!strcasecmp($type, "LONGTEXT"))
                {
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} LONGBLOB");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} LONGTEXT CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }
                else if (!strcasecmp($type, "TEXT"))
                {
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} BLOB");
                        MysqlError();
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} TEXT CHARACTER SET {$target_charset}");
                        MysqlError();
                        $set = true;

                        echo "Altered field {$name} on {$tab} from type {$type}\n";
                }

                if ($set)
                        mysql_query("ALTER TABLE {$tab} MODIFY {$name} COLLATE {$target_collate}");
        }

        // re-build indicies..
        foreach ($indicies as $index)
        {
                if ($index["unique"])
                {
                        mysql_query("CREATE UNIQUE INDEX {$index["name"]} ON {$tab} ({$index["col"]})");
                        MysqlError();
                }
                else
                {
                        mysql_query("CREATE INDEX {$index["name"]} ON {$tab} ({$index["col"]})");
                        MysqlError();
                }

                echo "Created index {$index["name"]} on {$tab}. Unique: {$index["unique"]}\n";
        }

        // set default collate
        mysql_query("ALTER TABLE {$tab}  DEFAULT CHARACTER SET {$target_charset} COLLATE {$target_collate}");
}

// set database charset
mysql_query("ALTER DATABASE {$db} DEFAULT CHARACTER SET {$target_charset} COLLATE {$target_collate}");

mysql_close($conn);
echo "

";