Nest less and use more functions.

awful.php

public function syncProducts() {
    $db = JFactory::getDbo();
    JLog::addLogger(
            array(
        'text_file' => 'com_example_product.syncerrors.' . date('d-m-Y') . '.php'
            ), JLog::ALL, array('com_example_product')
    );

    // get products that need to be added
    // UPDATED 1 feb 2015. No more Join, no more upper price limit. We are going all in @ IceCat
    $query = $db->getQuery(true);
    $query
            ->select('a.eancode, MIN(a.minimum_price) AS minimum_price, COUNT(shop_id) AS shop_amount')
            ->from($db->quoteName('#__example_product_affiliate_data') . " AS a")
            ->where("LENGTH(a.eancode) >= 13 AND LENGTH(a.eancode) <= 15 AND a.eancode !='0000000000000'")
            //->where("a.state = 1 AND LENGTH(a.eancode) >= 13 AND LENGTH(a.eancode) <= 15 AND a.eancode !='0000000000000'")
            //->where("a.eancode IN (5906720027783,8806086111171,8806086111126,8806086124164,8806086073134,8806086111157,8806086096911,8806086070232,8806086021104,8806862218382,8806085407800,8806085490031,8806085407916,8806085407992,8806085408036,8806085408371,8806085497276,8806085408395,8806085496477,8806085408418,8806085496422,8806085413122,8806071494647)")
            // below is bugged, because there are affiliate shops that don't have categories that fit.
            //->where("(a.category LIKE '%vaatwa%' OR a.subcategory LIKE '%koelkast%' OR a.category LIKE '%wasdrog%' OR a.subcategory LIKE '%witgoe%')")
            ->group("a.eancode")
            ->having("COUNT( shop_id ) > 2")
            ->order("a.eancode ASC");
    $db->setQuery($query);

    $productsToSync = $db->loadObjectList();
    foreach ($productsToSync AS $product) {
        if ($product->shop_amount < 2) {
            // The having clause means this is unreachable.
            continue;
        }
        $this->syncProduct($product);
    }
}

/**
 * One function, with one purpose
 *
 * Split out any chunks of logic to a separate function.
 */
public function syncProduct($product) {
    $productmeta = new stdClass();

    // Get extra info from icecat
    $icecatArray = $this->getArrayByEancode($product->eancode);

    // create functions to do specific tasks not public function doesEverything();
}