I think you will find it will be a series of choices based on your wants and specific items that appeal to you.
A summary of what I went with (or am still considering) to spark interest for you:
1. Security and Automation - Elk M1Gold - Security and automation panel. A favorite around here.
2. Lighting Control - Insteon - This is a heated topic. This is the cheaper solution. I have found it to work well once I got it setup across the house. This is tied to the elk for automated lights.
3. Thermostats - HAI RC80B thermostats hooked into the Elk so rules can trigger the heating/cooling
4. System Sensor 2-wire smoke detectors hooked to the Elk (although I would probably go with 4-wire if I did it again).
5. General Electric CO2 detectors - Nuff said
6. System Sensor Heat Detectors for the attic and garage - Hooked into the elk
7. CQC - Automation software. I have not finished setting mine up yet, but you should look at IVB's posts as I hope to one day have a setup like his.
8. Motion detectors - Mine are not in yet, to trigger events or for alarm. Internal/External. If you are building you might want to get opinions on Pulsar (I think they are called) sensors that go in the floor boards. Supposed to be very reliable but need to be put in when you build. I have no experience with them.
9. Irrigation controls - I have wiring from my sprinkler to the elk so that once I finish hooking it up it will control the sprinklery. Add rain/wind/freeze sensors as well.
10. Glass break sensors - To determine if a window has been broken
11. Driveway sensor - To sense cars coming onto your property
12. Camera's - Tied to other events to allow you to see the properly (i.e. when a car arrives, the doorbell is rung, etc).
13. Sound proofing - Acoustiblock or equivalent for soundproofing/insulation?
14. Keypads - I went with Elk LCD keypads (KP2), but they have nice touchscreens as well (~$1200).
I'm sure I am missing a lot, but that should give you some ideas. I did not even touch home theater yet. I am sure there will be no end to the posts though.