Obviously speaker wire to the location of all the speakers. For my rear speakers (and my fronts, because they are wall mounted) I put up 3/4" plywood to have something to screw the speaker mounts to and just drilled a hole in the plywood and pulled the speaker wire through. I did not bother with low voltage boxes. Some people run conduit instead and pull the wire later, I'm not sure this is worth the effort. Use in-wall (CL or CL3) rated wire. Monoprice 12 AWG seems like a good deal.
To the projector run 1 HDMI cable, 2 cat5e or cat6 cables (for HDMI via a balun if needed). This would be the absolute minimum. Extras would include another cat5e cable that can be used for a control wire (RS-232 or IR), 3 RG6 cables for component video and a 2" conduit for any surprises (like pulling a new HDMI cable). These cables obviously run to your equipment rack.
To your equipment rack you will want an Ethernet drop, cable or sat drop and power. Many people go for 2 circuits, 20 amps each. It probably overkill for most, but they're pretty cheap to do. I ended up with 4 20 amp circuits in my equipment closet so I guess I'm ready for anything!
One other thing to consider with wiring is home theater lighting. With dark paint or fabrics, these rooms really soak up light. It's nice to have several zones of lighting, all on dimmers, so you can have it bright enough when needed for cleaning and the ability to turn off the lights on the screen end of the room and still have some light over the seats during non-critical viewing. My room ended up with 6 zones of lighting, but you might find that even 3 or 4 zones of lighting adds something special to the room. And changing the lighting by remote control is cool! A Grafik eye can do this or the Infrared Lutron remote control dimmers could work on a tighter budget. If you got 3 or 4 of them you could have them all off, all on or all dimmed (different levels for each switch).