New home cat6 wiring and conduit
Conduit is always a good idea, in my opinion. Network/communications cable is something that has a much shorter lifecycle than a house. It's feasible, just requires application of money. If it's planned in from the design phase, that reduces the cost considerably .vs. retrofitting.

A house is not an office building, in most cases, so a single panel with every cable run to it is probably a more efficient layout than "patch panel per floor", as @Tyson commented.

Don't forget network to the middle of ceilings - the best place to put wireless access points, which work best when attached to wires.

As an aside, either use Cat5e or get Cat6A - Cat6 without the A is a cable that's only able to run 10 gigabit for short distances - at 1 gigabit, 5e is all you need.