My home is currently totally open. Just the outer walls and the roof. The studs are accessible in every room. I am planning a dedicated home theater,
14'-7" x 18'-6". I want to have structured wiring. Phone and data outlets in most rooms, audio and video distribution to at least 3 or 4 additional locations. Security, accessible through the Internet and some lighting control.
I'm going to need acoustic treatment in the theater. My plan there is to use double 5/8" sheet rock and green glue. I would like to future proof my wiring and run any additional wire I might need for different speaker placement etc.
I am even willing to put fiber in the walls for future use. (What kind of fiber?)
Perhaps touch screens for control and RF remote instead of IR. What kind of software etc. As you can see I am in need of any suggestions since I'm not knowledgeable. I am however pretty handy and would like to do as much as I can myself. Any help would be greatly appreciated. Thanks.

What is your deadline? I would run "smurf tube" to all locations you are considering. Running the tube allows you to run the correct wires later. Cat5e/Cat6 wire is fairly cheap and you can run almost anything over it... I would use several runs to each location for phone, internet, security, etc.
If you use a matrix switcher like the AVATrix, then you can use 2 runs of cat5 for your component audio and video as well. If you want to go with a traditional matrix switcher run 3 rg6 for your for your video and a good shielded speaker wire for your audio.

The best thing you can do is to make a plan. Identify EXACTLY what you want to accomplish. Then identify where things like TVs, touch panels, audio control, etc. will be placed in the room. Your decisions will affect exactly what cable you need and where your cable is run to. You will also want to pic a central location to bring all your wiring to...and bring the external phone/cable/satellite connections to this room as well.

I ordered most of my cable from Home Controls (http://www.homecontrols.com/cgi-bin/main/co_disp/displ/pgrfnbr/2/sesent/00)
1 (WR2R2C62FS) Bundled Cable, RG6 Quad Shield, Cat6, FiberOptic
1 (WRCAT5E10Y) CAT 5E Wire 1000FT, Yellow
1 (WR2R2CJ) Bundled Cable, 2 Cat5e and 2 RG6 Quad, Jacketed
1 (WRRG6DL10) Bulk Wire/Cable Quad Shield Coax, Siamese, 1,000'

I bought speaker wire and security wire at a local dealer.

and my "smurf tube" and low voltage boxes from Tri-State Electronics (http://www.tselectronic.com)
1 (SC100A-24) 1 Gang Low Volt Bracket 24 per pack
2 (SC200A-24) 2 Gang Low Volt Bracket 24 pack
5 (CATCR50) Caddy Cable Retainer 25 pack
1 (SCG4X1C-100) 1 1/4\" Resi-Gard Raceway 100 ft
50 (SCE943G) 1 1/4" Resi-Gard Male Terminal Adapt.
3 (21069) Nylon Cable Clamp .500" diameter 100 pack
5 (21029) Nylon Cable Clamp .250" diameter 100 pack
1 (VC9963SC) Resi-Gard Solvent Cement
11 (SCE977GC) 1 1/4\" Resi-Gard Raceway Clamp 5 pack

Prices are omitted... you will have to shop around for the best prices when you have a complete plan. I just included the product numbers and companies so you can look the products up for yourself and get an idea of what is out there. I'm sure many more people will chime in with great ideas for you. Hope it goes well :)

Where are you located?

My suggestion would be to find someone (probably local... check the CEDIA website) who can at least come out to the house and tell you what to do, what wires you need, and where to put them. We could all sit here and make suggestions, but seeing the house and talking to you personally is always a clearer and better way to figure out what you need and what you will need.

I would run cat6, fiber if you want, speaker wires/cat6 for speakers and volume controls throughout the house. For the dedicated theater maybe HDMI and COMPONENT. There's a lot to go into it and people get paid a lot of money to design it. You just need someone to design it and maybe only help with part of final install. Some companies may not be willing to do that. Good luck.

Should the cat6 be shielded? And which fiber do you suggest?

Cat6 is slightly shielded, but the really the only difference between Cat6's is if you get a Plenum Cat6 which is basically just Cat6 that's Fire Rated for commercial buildings. There is sometimes a quality difference between brands of Cat6/Cat5e. I'm not sure how much that particularly affects the system. I currently use Ice Cable Systems wire for all my applications. Unfortunately, I do not know much, if anything about which fiber to use. I do not do super high-end installs so my customers are not all that willing to install it. Try finding a local high end a/v outlet. They may be able to point you in that general direction.