When I design a wiring system, be it for a house or an office, I traditionally identify two key walls where someone might some-day put things; and account for rearrangement of the room (or re-purposing). So, in the master bedroom - people typically have a bed in an obvious place; they have a TV in an obvious place; so you know where to run the basics - but what if they someday need to put a desk/computer in there (you may have an office today, but what if someone else moves in or you have too many kids - or the next family moves in)... In functional areas, like a built-in desk or bar, you may someday want a media-pc or something accessible by the family. In kids rooms, expect that they may someday have a bed, TV, and computer desk. With those considerations in mind, I generally pick two opposing walls and put in my wiring there. For my last house, I did 3 RG6 and 3 Cat6 to each of those locations; it was overkill, but at the time DirecTV DVR's required two tuners plus I had basic cable and a desire to maybe use cameras and channel modulators in the future. (to back my point about new technology following what consumers typically have, DirecTV can now run dual LNB's for multiple tuners AND IP/network all over a single Coax).
Once those locations are identified, you can run smurf tube very inexpensively to the low voltage brackets... have these run someplace accessible - basement or attic. They don't have to home run all the way to your wiring closet, but that could be fun too if you want. Also, when pulling wires, it can be helpful to leave some polyline in the box/conduit along with the wires. It's cheap and makes things easier later.
For AV, you should have a couple key locations identified where you'll run media... maybe a basement, maybe a home theater, wiring closet, or even the family room entertainment center. From there, make sure you can add/change wires easily to/from your wiring closet. Chances are video matrix equipment will either be in your wiring closet or media center... unless you've chosen to pull all equipment in a central place in the house.
As far as lighting, engineering your own system won't be UL approved and quite probably not up to code; but there are plenty of players in the hardwire space. I know I like Lutron from what little I know - but there are better experts around here on lighting systems that can tell you the differences. I have seen them both ways - with everything run to a central load-controlilng bank and low-voltage to the switch locations, and I've seen several that have LV control wires coming off the switch that's otherwise wired like normal.
Good luck whichever way you go - it'd be fun to see you keep a blog or showcase updated.