What should I consider regarding LAN wiring before building a house?
First off, your cabling doubles as your telephone wiring, so 2 per room is reasonable. Put a jack anywhere you think you may need a phone, computer, or media device (TV/Boxee/game console/etc).  If you know you are going to likely need a couple at some particular spot (eg, a home office, or your main TV watching area) then you can do that as well.

Run all the cables back to some main wiring closet or utility room. The "nice" way to do it is with a patch panel, but you certainly don't have to go that far. You can get away with just terminating the ends with regular jacks. In your wiring closet, you'll have a switch of some sort (either the 4-port switch built into most routers, or something bigger if you need more than 4 ports). You'll also need a small patch panel for telco wiring for your analog phones. If you want a particular jack in the house to be on your network, plug it into the switch. If you want it to be telco, plug it into the phone panel. Note you don't need every jack to be active, and you don't have to decide telco or network now.

Here's how I have my house terminated, including patch panel. Note I have a 16-port switch, then the patch panel. There's only one analog telco line (port 4), the rest of my phones are VoIP (there are two power injectors on top of the switch for a couple of those phones). 





You may also consider running coax (RG-6) to TV areas, for use with cable or satellite, and you can terminate in the same boxes as network cables if you want. In my house, I have a box with 2 Cat5's and a coax in every room, but I would probably split them apart so there was one on each side of the room if I could. In my case, I was retrofitting most of the house and mostly just did interior walls. 



In my opinion, Cat5e is good enough (it supports gigabit), but Cat6 works too (I personally don't think it's worth paying any extra for).

I would not be overly concerned with noise in a residential setting. Twisted pair wiring is resistant to noise anyway. Try to avoid prolonged parallel runs (less than 6" apart), but even if you do you're not likely to notice any problems. 



As far as future-proofing, one word: Conduit. 

Who knows what cable tech will be used 10 years from now. Install what is useful today. If you want to run a 1 gigabit network, and a couple 1080p video links to a flatscreen on the wall, then install cables that can support that. By the time 4K or holographic video or whatever is "current" 10 years from now takes over, there's a good chance there will be new cabling standards and all the most expensive cutting-edge cables you can buy now will be obsolete. 

Case in point: 15 years ago, 10 Mbit was a common ethernet speed, and 100 Mbit was high-end. 802.3ab (gigabit over copper) was only introduced in 1999. 10 years ago, YPbPr component video was top-dog (HDMI only came on the market around 2003), and now it's getting hard to find gear that even has component video connections.

If you can afford it, sure, install Cat 6 or even Cat 7, but you have to realize any extra you spend on it is basically a bet that in 10 or 15 years, there is not going to be some new standard or totally different technology that makes it all obsolete. There's also a chance that you won't need it: I have gigabit throughout my house, but some of my (within 1-year-old) end-points (such as VoIP phones, and media streamers that play 1080p video) still only have 10 Mbit connections, because that's all they need.