skyking, I got the 3/4" blue conduit and snap-together boxes from Home Depot and it was incredibly easy to do. Frankly it was only a very slight more work than pulling cable bare(*). I actually did the cable installs after closing having the conduit in place. I strongly recommend conduit to everyone.
(*- okay, there was one place that was much more difficult than bare cables - my main heating plenum, I didn't use flexible conduit, I used a lot of 2" PVC pipes, and many 2" pipes times about 30' of length is a pain to work with. Most people will be fine with a couple of the blue flexible conduits and that will be much easier to work with!)
jntdesign, cat5e should be enough for gigabit Ethernet if properly installed. cat6e will be better for gigE. One of the reasons for the conduit is that you could do the cat5e now and if you had runs that weren't working for gigabit and you wanted to use them for gigabit, you could later replace them with cat6. If you're looking to future proof your home network, conduit will help more than cat6.
As far as plenum vs. riser, I have heard conflicting things. I did plenum for my second floor, all of which was home run through my plenum (I also ran over-cat6 cable, so I took the highly expensive route - just in case you're wondering. If cost is no object, do that. But cost is typically an object!).
I know enough people who understand well what plenum vs. riser means and chose to do riser that I believe you can get away with riser. Plenum is the safer/more conservative choice, but is also twice the cost. The bottom line is as skyking said, no other wiring in your house is plenum rated and when it burns the cat5/6 cable is going to be the least of your worries. Plenum does buy a little more piece of mind, though - if you use plenum and didn't have to, the only downside is cost (well, and the jacket's often a little harder to work with). If it's only $50-$100 or so difference maybe that's worth it to you and yours.
As far as how many spools/boxes, it's best IMO to have one spool per cable that goes into a bunch, so you can spool them out in parallel. I prefer real spools to boxes because I'm old fashioned... and I have spoolers
A couple of chairs and a pipe makes a reasonable low-budget spooler in a pinch. But anyway, put them in parallel and pull out what you need, and they're more or less equal length and ready to go. I'd also suggest you plan on buying more and not less.
If you need a run of 75' and you've got 50' left on the spool, that 50' is waste even when you get another 500' spool - better to have longer spools so there are fewer forced cuts. Unfortunately, you can't take it back, but you will use more cable than you plan on no matter how much you pad, and leftover cable is plenty useful anyway if you know how to crimp (where's JackMDS and his "DO NOT CRIMP"?
. And anyway, 1000' spools are the typical unit of sale and often the cheapest per foot - put another way, you'll pay a slight price premium per foot for a 500' spool, a slight price premium for a box rather than a spool, and if you need a custom length you can get downright ripped off if you're not careful.
As far as value on your house, I think you will get some value out of having Ethernet jacks wired. I don't think you will get any value out of the delta between a minimal wiring job and a high-end wiring job (better cable, plenum, etc.), so when doing anything more than the minimum, do it for your needs and not as investment.
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