Think about your needs, your gear, the rooms you want gear in, etc.
I wish I though about this when we built but we did not.
Your primary gear location should have a dedicated electrical line to the circuit breaker box. There should be the cable line and ethernet line as well as enough electrical outlets to bring current and signal to your primary location.
You will also want to think about other video/audio connections from here to other rooms. You probably want ethernet, speaker, probably hdmi lines from the primary location to each room you will want an audio/video connection from your primary gear to each room/area.
You may want speaker wiring in the ceiling for whole house/outdoor audio...useful for entertaining etc. when you just want decent background music rather than your HT speakers.
I'd suggest speaker wire for the fronts, surrounds, sub and in case...rear surrounds, second sub, height speakers in the primary location.
Next would be signal the other rooms that will have video/audio gear.
If you will have any wall mounted tv's you will want a current/signal box mounted on the wall where the tv will mount over it. This box should contain an electrical outlet, cable coax connector, ethernet conn and probably an HDMI connector. If you are going to use external or wall mounted speakers you will want wiring and connectors from the primary location to each room.
Many who have this opportunity use PVC conduit to hold these wiring/cable runs to allow for changes/additions in the future without having to go back into the walls.
Remember this...it is much less costly and aggravating to do this now than after the walls are up and you are living in the house and start saying "woulda, coulda, shoulda".
Draw out a diagram of the house and rooms. Pencil in the locations of your current gear and future possibilities. Detail the wiring types needed for each room and pencil them in. Add the outlet connectors for each wiring/connection. Talk to the contractor about use of conduit for the runs, at least the primary wiring runs.
If this person is experienced and good at what he/she does you will also get other suggestions/recommendations as well. Think about them carefully. An extra $500 now will be well worth it when you just connect a new device 2 years from now and all your wiring is in place just waiting.
Good luck, take lots of pictures and keep us involved. We love this sort of stuff.