As far as meeting a specification, there are no grey areas.
Cat 5 works just fine for telephone use, an RJ11 (phone plug) plugs very nicely into an RJ45 (data jack) socket, though it is kind of a schlocky way to do things. Since you can use Category-rated cable for phone, but you can't use phone-rated cable for data, cable everything with category-rated cable. Get at least two runs to every location. While you're at it, have the contractor run two runs of RG6 to the same place. There are outlets that will acommodate both type and still look nice (for the missus).
You absolutely should not use phone and data in the same cable
Have all the cables route back to a single room. The laundry/utility room/ corner of the basement is fine. Make sure there is also a power outlet (idealy a Quad) in that neighborhood, so you can plug in a hub/switch/cable modem/dsl modem, etc. Also make sure that a good ground is available (should tied to the same grounding point as the electrical service.
Also while they're at it, have them pull some RG6 from the most likely place to mount a satellite dish. If you really want to hedge your bets, have FIVE runs of RG6 installed to the possible dish location.
You might want a run or two of coax into the attic (indoor antennas (FM/VHF/UHF)).
All of the cables from all of the rooms come back to one place, one panel (per media type). Then you can cross-connect anything in the house to any other thing in the house....it's a wunnerful thing.
I have a townhouse. I had two Level-7, two RG6, and four strands of multimode fiber run to each location, two locations per room (opposite corners), and one room (the second bedroom/"computer room") got four. I have outlets (data and power) in some of the closets (in case I want to tuck a server out-of-the-way) and two UTP and two coax to the garage (phone and TV for the wood shop). I had a 20 AMP quad outlet split-wired (two different 20 amp circuits) in the utility room where my switches and stuff are located (on a 1.5KVA UPS). Shoot for ~24 as a magic number. Most panels come with at least 24 ports...might as well use 'em all.
Cable is cheap, the labor is cheapest when done on naked walls. It will add only a couple bucks per month to the mortgage.....GO for it! You may want to consider having cable pulled everywhere, but only terminated in the locations you're most likely to use in the near future. Listen to the voices in your head.....more cable is good cable......adn remember, it's good for more then data networking...I use some of mine to distribute A/V. If you're likely to use a multi-zone A/V amp, you can distribute the zone info over the same cable plant...
FWIW
Scott