Main thing - get multiple bids, don't
contractor. Big range of prices.
As far as equipment goes, choosing the right sizing of units with the most energy efficient models is key. For example, house i used to live in had 3 ton AC. Ran continously during the day in the summer and couldn't keep up with the heat. For the size of house it should have been a 5 ton unit.
Most furnace brands are decent, Carrier or Trane are good AC, used by most commercial and industrial buildings.
If you have asthma or allergies it might be worth it to pay extra for built-in electronic air filters.
Make sure if yours isn't to get a new Energy Star rated digital thermostat too.
Ductwork generally doesn't need replacing, but should be cleaned out periodically.