There's a similar thread you should go read:
Wiring a house
I would suggest you put in conduit and boxes that snap to the conduit if you have the ability to do so. Then it's much easier to change wiring later.
Cat5e vs. Cat6... it depends on how much you plan on running gigabit, and how cost sensitive you are. If you aren't thinking about gigabit in a serious way, go ahead and put in good cat5e (Berk-Tek LANMark 350 for example, which is ca. $100/spool for CMP). If you put in conduit (see above), you could upgrade the cable on specific drops in the future if you found that the cable was limiting you, but you could first try upgrading the terminations. If you are serious about gigabit or want the best/most future-proof, put in the best over-cat6 you can get (Berk-Tek LANMark 2000, which is ca. $225/spool for CMP, and use Ortronics Clarity6 jacks. This is what I've got

).
I would run communications separate from the rest and in separate conduits if possible. Coax really shouldn't crosstalk with UTP, but other analog might. I just like keeping digital and analog separate (which I then violate by running POTS over the UTP...). Also, this gives you more flexibility to choose particular cables, not having to get what's available bundled. Incidentally, consider running speaker wire.
I would not recommend fiber. Fiber terminations are expensive, the tools are expensive, and the required knowledge level to do them is higher. Oh, and pulling fiber is trickier than pulling copper. And for what? You can do gigabit Ethernet over copper, and that's starting to be the dominant way to do it. Also, contrary to popular belief, fiber is not the be all end all, there are limits to what fiber can carry and they're constantly improving that, and so like UTP it turns out that old fiber can't be used for the latest and greatest application. The fiber you're thinking about running in your home will probably not carry 10Gb/s Ethernet, for example. So don't buy fiber just because of the incorrect belief that it will give you massive future-proofing, only buy fiber if you know you're going to use it..
Where to buy cables? For high-end cables and terminations, I buy from Anixter. You will need to find your local sales office and then you will have to find someone there who actually wants to take your money (their sales guys often have problems with this concept).
For more mass-market cables, I'm sure others on this forum will be able to offer better suggestions. If you just want generic Cat5e (which, if you're doing conduit, would be okay), check out your local Home Depot, and there's a deal at compgeeks.com (see Hot Deals).