I highly recommend Monoprice, I have used many different wires over the years and I recently used some of their Solid Core / Plenum Rated wire and I am so impressed with the quality of it. I was able to get 1,000 feet of it for less than I paid for 500 feet of Beldin which is also a great / high quality bulk wire.
Keep in mind that if you are running wire through / inside walls you need to make sure you check your local building code(s) and make sure you get the proper wire. This might not seem like a big deal now but sometime down the road if an electrical inspector comes in the house and sees it they can make you pull it out. Yes I know it is unlikely to happen but why not spend the money now?
Personally I like to terminate all of my connections in to a Patch Panel / Jacks, it is easy / clean way to go and if anything ever happens to the jack you just need to replace it. That is unusual as you usually will just have to replace the jumper you have connected from the Patch panel / Jack to the Switch or device.
Again I would suggest Monoprice, check out their "Modular" Patch Panels and jacks, they are very inexpensive and work like a champ. I would however avoid using their "Tool-less" Models as I've had no luck with them at all. Also as a side benefit using modular jacks allows you to color code things if you so desire. This is very useful especially if you are running more than one jack to a room or plan on having different networks.
Finally remember to LABEL EVERYTHING with as much detail as possible!!! Trust me you will thank yourself later on down the road.
Here's a few links from Monoprice for the items I mentioned...
Bulk Cat 5e / Riser Rated
http://www.monoprice.com/product?p_id=878
Modular Patch Panel
http://www.monoprice.com/product?p_id=7260
Keystone Jacks
http://www.monoprice.com/product?p_id=5376
Of course you can also go with Cat 6 if you so desire, always think of future expansion!