Trade-offs between Job Queue vs. Drupal Queue
Drupal Queue is a backport of Drupal 7's queue API for Drupal 6. It provides basically the same features as Job Queue. However a big advantage with Drupal Queue is that it uses the same API as Drupal 7 Core. This means if your module uses Drupal Queue in D6, your upgrade path to 7 will be effortless.