Look online at the pricing of cable. I believe that Cat-6 is designed around gigabit ethernet which is the direction I would go. I'm not sure you can even find non Cat-5e cable anymore (cat-5).
The price difference really shouldn't be that great on a box of 1,000 feet of cabling.
eBay has 1,000' spools for about 100 bucks. So, I would definitely go the cat6 route.
For punching down the cable, it is pretty darn easy and you can find numerous online sites that can walk you through it... But, like I said - it is easy. I picked up a metal tool that works better than the freebie that comes with some terminals for about 7 bucks at Home Depot. Not as nice as a real punch down tool, but works fine for my VERY limited needs.
I would go with 568B wiring inside a home. If you Google 568B you will find more than a few places to let you know what exactly we are talking about.