I went with Cat6. At least two runs to every location, with all locations coming back to a central closet. You may want to talk to the electrician about putting an extra power recepticle (20 amp would be nice) in the closet near the termination point as well, so you have the extra juice for hubs/switches/cable modems, etc.
Also have them run an extra pull to the box outside (at the phone demarc):It makes it a little nicer if/when you get DSL or possible other future services installed, and keep it separate from the phone.
Also do two runs of coax to each location. If you're using a DSS dish, having the extra coax is a real blessing, especially if you're looking at doing a Tivo (dual tuner). Also don't forget to have them pull a run or two of coax to the attic, in case you decide later to hang an OTA antenna (most areas are broadcasting some flavor of digital TV, and in 2006, they all have to).
If the budget allows, have them (at least) pull a run of four-strand fiber to each location (and one to the phone demarc or near it). Even if you don't terminate it, the future seems to be moving to the eventual use of fiber everywhere. The cost to pull all of the media is gonna be about the same as pulling one run, the media is not that expensive...termination is usually the big kicker cost-wise (labor and materials).
The other ssuggestion I'd offer up is to use standard panels, not the "Home Cabling" boxes with all the goofy inserts. They never seem to have the room or inserts you really want, and they're not generally available. If you go with a wall-mount rack and regular panels, the troubleshooting is much easier, it'll be much easier to upgrade, and parts are available just about everywhere.
FWIW
Scott