The {system} table has been removed

If you were running any queries against the {system} table, these won't work any more. For example:
Drupal 7:

  // Enable the admin theme.
  db_update('system')
    ->fields(array('status' => 1))
    ->condition('type', 'theme')
    ->condition('name', 'seven')
    ->execute();

Drupal 8:

  theme_enable(array('seven'));

Setting module weights:
Drupal 7:

  // Set a module's weight.
  db_update('system')
    ->fields(array('weight' => $weight))
    ->condition('name', $mymodule)
    ->execute();

Drupal 8:

  module_set_weight($mymodule, $weight);

To set a module's weight relative to another, a module_get_weight function is planned.