Comment Where to begin ... (Score 4, Informative) 336
I highly recommend you check out CocoonTech.com, especially the forums, as there are thousands of folks who have done this, and can bring you up to speed pretty quick. There is also a guide on the site (Wiring your home 101) which will tell you what wires you should run assuming budget isn't an issue (this lets you pick and chose what wire really matters to you).
You have so many options, it really depends on the time you are willing to put in, budget, and features you want.
I recommend you use an Elk M1 or HAI Omni Pro II security/automation panel as the 'core' of your system if security is really important to you, or if automation is your main vice, then look at the SmartThings, Vera, ISY-99, and HomeTroller (Zee) hardware controllers.
Most of us top this installation off with a software component, so we can bridge/interface many protocols and technologies (this way you aren't stuck with just one solution). Most popular commercial software solutions are Homeseer and CQC, but there are many alternatives, free, open source, etc.
Currently, Z-Wave, INSTEON, UPB, ZigBee, and WeMo are the popular protocols.
If you have the budget, consider hardwiring your home automation light switches, as the wireless/powerline based solutions aren't perfect, plus you have to worry about latency/security. CentraLite, Crestron and Lutron RadioRA are popular commercial solutions. They usually require dealer/installer access, but if you really look around, you could get access to the hardware (I'd probably combine RadioRA with a HAI/ELK panel).
There is so much more to tell, so if you have any other questions, ask away, and don't forget to check out the CocoonTech home automation forums!