Okay, first of all, for a home user I have to disagree on the managed switch. It's adding a lot of complexity that you just don't need. Just get an unmanaged gigabit switch with Power over Ethernet (802.3af, you'll see why later)
Second, regarding CAT6, it really has no advantage over CAT5e today. CAT6 is needed for 10 GigE Is it more future-proof? Maybe. But 1gbps of data to every room is a heck of a lot of data I can't imagine you needing to exceed in the lifetime of the wiring to be honest. Not only that, but 10 GigE on normal CAT6 can only go 55 meters, not 100, so you could possibly bump into the distance limit, though it's obviously very unlikely in a house.
Third, specific equipment recommendations - I've had VERY good luck with EnGenius products EXCEPT the EAP300 (I'm working with EnGenius on that now, so I save my review for a bit, it's been problematic though). I'd get an EnGenius ESR750H router and two EnGenius EAP350 access points (unless you can wait for the EAP600 to come out later this year - dual band and prettier).
Why am I recommending those instead of another, better, dual-band AP? Well, dual-band just isn't that needed for a house and a ceiling-mount Power over Ethernet AP just has a much better aesthetic value in a new house. EnGenius has a much improved model coming out soon, the EAP600, so if you can wait to buy until the house is built, wait for those to come out.
Run CAT5e to the ceiling and then there's no visible cabling or anything. Your APs should be arranged one on each floor, using OPPOSITE CORNERS (not one in the middle of each floor - basically think of balls of coverage). Use channels 1, 5, and 13 for each AP, saving channel 9 (the remaining non-overlapping channel) for any future outdoor coverage or the like. Use channel 13 on the MIDDLE FLOOR - some American equipment will not allow you to even connect to AP's on 13 (some Android phones are one example), so that ensures any visitors/imported gear will still get OKAY signal though maybe with some dead spots. This really bugs me, since it's up to the network operator to assure legality. Most newer equipment seems to follow that rule, allowing cards to connect to whatever channel they see, and trusting the network that it's legal. But not all. Also, Macs (but not iPhones/iPads) are weird - they look at the set regulatory domain of what they do see to determine what to scan. So if you have a neighbor with an imported router set to North America your Mac may not see your channel 13 AP!. That won't be an issue if YOU have more than one AP and have your AP's set to a European regulatory domain, but for some people it is an issue. And it's stupid. Apple should passively scan everything and connect to what it sees... just like on the iPad/iPhone... UGH.
Anyways, hope that's of some help.