Greetings!
Everything comes down to personal preference; during preconstruction it's nice because you can do anything you want...but technology will change later.
My basic advice is to run things to two near-opposing walls in each room - like my last house (major overkill) had 3x Cat5 and 3x Coax in a plate, and I had these plates on opposing walls of every room. I barely used a fraction of them. This current house was already built and very difficult to add to, so I'm getting by just fine with a single Cat5 per room. The market caters to the largest market segment - and that's people with zero to minimal existing cabling... so where DirecTV used to need 4 Coax + an ethernet, it's now all a single wire; TV's are coming with wireless built in now!
The good news is that more and more will run over IP now, not just Cat5 - so I have TV and Internet everywhere I need it; the worst I had to do was buy VLAN-Capable switches so I could separate my networks out better over that single port.
Anyways - if you know of things like Video, either run it now or - better yet - put in conduit or smurf tube. One decent HDMI over CatX converter will cost about $500 for one that actually works... but if the conduit is there you can buy a rapidrun cable for $75 and be done... That said, you're right - just about anything else can be done with Cat5 (there's nothing that even requries Cat6 in the residential market yet). Run what you can think of, without locking yourself into a particular furniture configuration (kids rearrange rooms all the time!); and make sure you leave yourself some room to make changes; access paths, conduit, etc - are all handy.
And I'm completely with BSR regarding security cabling - use the right stuff; and that's where you might forget things. If you already have the HiFi2 you'll probably stick with HAI for security - I don't know their requirements, but some of the less common runs I had were - doorbell sensor; garage door sensors and triggers; gate sensors; wire for speakers inside the house; wire for strobes; things like that... For smoke detectors, if you do that, you need to use fire-rated wire (and per UL there's more restrictions, like at least one keypad connected via fire-wire, and some other).