Originally Posted by ccbadd
Keep in mind that a good switch can give you very high back plane throughput. Two switches exchanging data over a single GigE port will not perform nearly a good as one larger switch transferring data across a multi-gigabit backplane. I use a 24 port managed switch with 48 gigabit backplane and bring all drops directly to the switch. I recommend using a single large, preferably managed, switch and pull cat 6.
In most home environments, you won't be communicating among computers, you will mostly be sharing a connection to the outside world. The exceptions are printers, NAS, and media servers. Design so that you directly connect the media source with the receiver/device that is streaming it through a good switch (not hub).
Run 3 to each room (see bobsilver, above), 4 to an office or media room. In the case of the office, it is nice to have a port for a desktop, printer, phone, and even a wireless AP without having to have an ugly hub/switch.
Run CAT6, but remember that the CAT6 standard is not simply the construction and materials of the wire, it also encompasses the terminals and the actual connections.
Don't run RG6 except service entry, dish, cable modem, or media closet. It is a total waste to whole-house wire with RG6, and the money is better spent on a better network.
Run a length of CAT6 to the ceiling at the top of the stairs and install a "smoke detector" wireless AP using POE. Wireless APs are ugly as crud and it is the clean way to get a great signal. Spend time thinking about where you are going to put APs before you close the walls. It may suggest random places for running wire!
Here is a post I wrote a long while ago with some hard-won tips on wiring: http://www.avsforum.com/t/1273786/20-tips-from-a-first-time-whole-house-wiring-veteran