Depending on how your house is laid out, I'd just run the cables you need for now but plan on upgrading the system and add more later, if needed. If you have a single story house and have access to each room from a basement then running cables from below is relatively easy. If you have a two-story house the you'll need some sort of raceway between the basement and 2nd floor to run cables from the basement to your upper levels.
Run the wiring from the basement to the attic and then drop the wiring through the walls from above. Get some low voltage wiring boxes, which are nothing more than an open plastic frame to which you attach the outlet plates and covers. Don't use standard electrical boxes because adding more wiring becomes a difficult job if you have to deal with a closed box.
Find a central location where you can mount your multi-switches, distribution panels, etc., and run everything from there. I have a huge return duct on my 2nd floor which I use as a wiring closet. It's nothing more than a large open area behind the wall between my bedroom and laundry room on the 2nd floor. I got lucky and was able to create a direct path from there to the basement to run my wiring. I have a heavy nylon string that I have run through the raceway and tied off at each end. It's a simple task to run wiring by tying the cord to the end of a cable and then pulling it through from the other end.
Before you run off half-cocked and run all the cables everyone is suggesting, decide on how you plan on distributing the signals to each location. Decide what sources your currently have and potentially what you might need down the road. Chances are you'll only be half right anyway since technology and delivery systems change faster than most of us can keep up with it. At a minimum, however, I'd run at least one cat6 line and two RG6 cables to each room. Forget about using cat5 or cat5E because you'll want to set up a gigabit network and cat6 is required for that.
If you're thinking of going Blu-Ray and have more than one HDTV you might want to consider setting up a Home Theater PC with Vista Media Center. You can get Media Center Extenders for use in other areas of the house that will allow you to access the main HTPC from any location. I have a server set up with my HTPC and I can access it from anywhere on my home network. I rip all of my Blu-Ray, HD-DVD, and standard DVD movies to the server using AnyDVD HD and stream them over the network to remote PCs for playback using one of several playback codecs. The Vista Media Extenders should allow you to do basically the same thing without the need for a separate PC at each location. You can also incorporate tuners into the HTPC and use it as a DVR to record any OTA programming or in-the-clear QAM channels on digital cable or FIOS. A Tivo is probably still your best bet for recording any encrypted programming and satellite channels.
