How to select all DB data and make a count of repeated words?

What you describe can be done via MySQL without recourse to PHP.

Given the way you have records, my suggestion is to use a temporary table to insert a record for each value that is separated by a comma and then select from that temporary table with the count:

CREATE TABLE minhaTabela
    ('id' int, 'nome' varchar(100), 'tags' varchar(255))
;

INSERT INTO minhaTabela
    ('id', 'nome', 'tags')
VALUES
    (1, "Gabe♦", 'Php, Mysql, Java'),
    (2, "bfavaretto♦", 'MYSQL, Apostila, Java'),
    (3, "utluiz♦", 'Microsoft, C++, Java'),
    (3, "John", 'C++, Apostila, Java'),
    (3, "Doe", 'Apostila, Mysql, Java')
;

CREATE TEMPORARY TABLE temp (val CHAR(255));
SET @S1 = CONCAT("INSERT INTO temp (val) VALUES ('",REPLACE((SELECT GROUP_CONCAT( DISTINCT 'tags') AS data FROM 'minhaTabela'), ",", "'),('"),"');");
PREPARE stmt1 FROM @s1;
EXECUTE stmt1;

SELECT val, count(*) FROM temp GROUP BY LOWER(TRIM(val));

Result obtained:

SQL Fiddle

┌───────────┬──────────┐
│ val       │ count(*) │
├───────────┼──────────┤
│ Apostila  │    3     │
├───────────┼──────────┤
│ C++       │    2     │
├───────────┼──────────┤
│ Java      │    5     │
├───────────┼──────────┤
│ Microsoft │    1     │
├───────────┼──────────┤
│ Mysql     │    3     │
├───────────┼──────────┤
│ Php       │    1     │
└───────────┴──────────┘

To use on the PHP side using PDO:

/* Dados da ligação à base de dados
 */
$dbcon = array(
    "host"     => 'localhost',
    "dbname"   => 'minhaBaseDados',
    "username" => 'utilizador',
    "password" => 'password'
);

/* Ligar à base de dados
 */
$dbh = new PDO(
    'mysql:host='.$dbcon['host'].';dbname='.$dbcon['dbname'].';',
    $dbcon['username'],
    $dbcon['password'],
    array(
        PDO::ATTR_PERSISTENT               => false,
        PDO::MYSQL_ATTR_USE_BUFFERED_QUERY => true,
        PDO::ATTR_ERRMODE                  => PDO::ERRMODE_EXCEPTION,
        PDO::MYSQL_ATTR_INIT_COMMAND       => "SET NAMES utf8"
    )
);

/* Ler os dados para uma tabela temporária
 */
$sql = "
CREATE TEMPORARY TABLE temp (val CHAR(255));
SET @S1 = CONCAT(\"INSERT INTO temp (val) VALUES ('\",REPLACE((SELECT GROUP_CONCAT( DISTINCT 'tags') AS data FROM 'minhaTabela'), \",\", \"'),('\"),\"');\");
PREPARE stmt1 FROM @s1;
EXECUTE stmt1";

$sth = $dbh->prepare($sql);
$sth->execute();
$sth->closeCursor();

/* Recolher a informação
 */
$sth = $dbh->query("SELECT val, count(*) AS total FROM temp GROUP BY LOWER(TRIM(val))");
$sth->setFetchMode(PDO::FETCH_OBJ);

while ($row = $sth->fetch()) {
    echo '<p>A palavra '.$row->val.' está repetida '.$row->total.' '.($row->total==1?'vez':'vezes').'.</p>';
}

/* Matar a ligação e o script
 */
$dbh = null;
die();

Suppose the $registros array is the records you pulled from the database. We will create a $tags array with the count for each tag.

$tagCount = [];
foreach ($registros as registro) {
    $tags = explode(',', $registro['tags']);
    foreach ($tags as $tag) {
        $tag = trim($tag);
        if (!isset($tagCount[$tag])) {
            $tagCount[$tag] = 0;
        }
        $tagCount[$tag]++;
    }
}

Then just order:

usort($tagCount, function($a, $b) {
    return $a > $b;
} );