I don't know if it still works this way, but in the 2005-08 period, I would often find air+hotel deals costing much less than just the airfare alone. This would happen when the flight loads were light, but the 14 or 21 day advance purchase deadline had passed. By buying the package on Expedia or Travelocity, you were basically able to bypass the advance purchase restriction and get the cheaper fare buckets at the lower price. It wouldn't work when the flights were full, though, and the lower fare buckets were sold out.

Buying this way, I always earned full air miles and elite-qualifying credit, but never earned any hotel points.