You are at a perfect time to do wiring since the walls are not up. I would recommend, if you are up to it, wiring two separate locations in every room. This may seem excessive, however if someday down the road your computer needs change you will already have the infrastructure in place and will not need to pay anyone to crawl around your attic and drill holes and run cable. The wiring could also be used for other needs such as video (on demand movies etc) and even phone. CAT5e wire should be perfect as the others have said. As to how to wire them, you would run a separate cable (called Homerun) to a central location, typically where your Cable, Satellite, or DSL modem are. There would be "loads" of wire with this however, but it is far worth the effort now when you have easy access, than to try to run a cable a year or so down the road after furniture and painted walls, insulation etc are all in.
In my case I homerun all my cables to a shelf I built in my Landry room. I also ran my coax cable to my Landry room. So all my network gear is in a single convenient place out of sight. Wife was happy because I put a clothes rod below the shelf so we could hang up clothes after they came out of the dryer (double bonus he he)
If you were planning on doing the wiring yourself, you would need the tools that burnyd and ristau stated. You would also need the faceplates and mudrings.
If you are involved in the building process, there are two phases, the Rough In phase and then the Trim Phase. During the Rough in, you install your mudrings on the studs in the locations you want your data. Mudrings look just like an electrical outlet box, except they are not an enclosed box like electric. They are either nailed on or screwed onto the stud. Next run the CAT5e cable, be sure to mark the cable on both ends like, 1, 2, 3 etc for each run. That way you can identify the cable later and know which cable is which. Run your CAT5e cable down the stud to just behind the mudring. Leave about a foot or more cable behind the mudring so you have enough slack to work with later during the trim phase. Tack the cable down on the inner stud being careful not to nick the cable. This is done so the sheet rockers do not pinch your cable between the stud and the sheetrock when they put it up. The sheetrock people will cut holes for your data box just as they would for your electric.
After the walls have been painted, you can do your trim phase. This is where you pull out your one foot (or more) length of cable and then terminate it with an RJ-45 jack, then put the jack in the face plate and put the faceplate on to the mudring. If you ran additional cables but don’t plan on using them now, just put a blank faceplate in that spot and leave the cable in the wall for later.
On the other end, the central location side, you would have to punch down the CAT5e cable to a patch panel. There are many sizes you can choose from depending on how many cables you ran. Most homes can get away with a 12 port. If you have less you can put in a dual gang mudring and get a dual gang faceplate to snap in your RJ45 jacks here as well. Dual gang faceplates can be found from one jack up to 12. The more cables on a dual gang faceplate the messier it looks however (is messier a word?) That is why a patch panel would be better if you had more cables. If you really want to have a nicer set up both Home Depot and Lowe's sells "in wall" enclosures that you can attach to the studs. these are real nice because everything is inside the box that is flush with the wall and has a door to hide all the cables. (not so good for active devices (powered) however as there is no air flow, these devices can over heat easily)
The specific way to wire them is typically TIA-586a (a specific wire scheme) for residential. You can do a google to get a nice color picture of this. 586a will work as a phone jack if you had more than one phone line in the home. (I could get into the phone details on this if you like, just let me know)
Hope that helps, post any questions if you have any more.
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