Magento – Fix Product Not Appearing in Store View

Here are some things to try that will help narrow down the cause of the problem:

1. Try using the default catalog/product/list.phtml template instead of your custom one
2. Try a different category or create a new one if necessary

If you post your catalog/product/home.phtml the community may be able to better assist you.

EDIT: The cause of the problem in this case was that the category was either a root category or outside the website/store scope - moving the category inside the current store's default category solved the problem, see comments below.

OP noted that setting the website IDs seems to resolve the issue:

$products = Mage::getModel('catalog/product')->getCollection();

foreach($products as $product){
    $product->load();
    echo "Disabling product: ".$product->getSku()."\n";
    $product->setStatus(2);

    $product->save();

    $product2 = Mage::getModel('catalog/product')->load($product->getId());
    echo "Enabling product: ".$product->getSku()."\n";
    $product2->setWebsiteIds(array(Mage::app()->getStore(true)->getWebsite()->getId()));
    $product2->setStatus(1);

    $product2->save();
}