You are asking good questions. Read a lot and consult with prewire folks. I was going to do my own prewire but decided to turn that over to others. I bought all cables - quite a bit from Monoprice and can generally recommend them. I used Monoprice CAT6 and it was stiff however and hard to work with. I had to redo a number of connectors as some didn't test well with Monoprice Cat 6 connectors. It was a big pain. Cat5 would have been much easier.
Are you doing alarm, home automation, whole home audio, Satellite/Cable, camera surveillance, telephone, lighting control, HVAC control, video intercom, etc? I did all the above and some of it is still a work in progress 6 months later
I have all equipment in my equipment closet including all set top boxes, HTPC, DVD, receivers, cable modem, gigabit switch, etc. I am now searching for a 4x4 HDMI matrix switch and can't recommend one yet, other than to say the Monoprice did not work. I'm now looking at Gefen. I like the HAI system I used for much of the home automation. It is great for alarm and for energy savings with lighting and HVAC.
My personal prewire list included:
Speakers: 16/4 jacketed cable - to all speaker locations including outdoor locations
Double RG6 to wall locations in most rooms - one for Satellite and one for Cable TV - include 2 RG-6 runs to exterior satellite dish location and 2 to telephone box for Cable TV
4 outside cameras to mud rings in overhangs - run 2 CAT5 - one for video balun/ triple power pairs and one can be for future IP camera with PoE. Coax and power lines are NOT NEEDED for cameras any longer unless the runs are well over 100 feet each.
CAT6 - 2 outlets per room (use quad plates with phone, ethernet and 2 coax)
Intercom - CAT5 and 18/2 DC to 3 interior color montors; CAT5 and 18/2 AC 24V to front door camera/bell
Whole house audio - 8 CAT5 runs to volume/selectors, 8 CAT5 runs to remote audio input/IR plates
Phone -run CAT5 to 14 locations
Run 22 ga HDMI cables to 3 TV's - 30 feet, 50 feet, 70 feet, also run 6 CAT6 to these same 3 locations to future proof for 3D/HDMI 1.4
Install three 36 inch in-wall structured wiring cabinets in equip closet
Install 22/4 and 1 CAT5 to 4 keypad locations and touchscreens
CAT5 to two thermostats. CAT5 to 3 remote temp sensors including attic, equipment room and outdoor sensor.
Orange plastic 2" conduit through ceiling headers at various locations for pull strings/ future proofing
Install wiring for 4 PIR, 4 heat/smoke detectors, 1 siren, 54 contact switches, 2 garage door switches, 8 moisture sensors
RG6 to 2 subwoofer locations
CAT5 to automated main water shutoff valve
good luck with your project.