What is the D6 equivalent of D7's hook_filter_info?
In Drupal 6, filter modules just implement hook_filter(). In particular, to process text from a filter, you should use code similar to the following one.

$result = module_invoke('markdown', 'filter', 'prepare', 0, -1, $input);
$result = module_invoke('markdown', 'filter', 'process', 0, -1, $result);


I assume the delta for the input filter is 0, which means selecting the first input filter implemented by the module.
The first call to module_invoke() could be not necessary, but most input filter prepare the text that is going to be preprocessed, mostly to avoid conflicts with other filters, including the ones implemented by Drupal core. In fact, check_markup() uses the following code.

// Give filters the chance to escape HTML-like data such as code or formulas.
foreach ($filters as $filter) {
  $text = module_invoke($filter-&gt;module, 'filter', 'prepare', $filter-&gt;delta, $format, $text, $cache_id);
}

// Perform filtering.
foreach ($filters as $filter) {
  $text = module_invoke($filter-&gt;module, 'filter', 'process', $filter-&gt;delta, $format, $text, $cache_id);
}