At least one 48" wide door into the house and make any hallways or stairways at least that wide for moving couches and stuff around. 

For the garage go at least 30' deep and use a seperate door for each bay, the wide single doors are a joke unless you drive a Mini Cooper or Smart car.  I'd put a drain in the garage.

I'd use a 1 piece bath tub/surrounds in the bathroom and make the bathroom big enough so that if you ever want to remodel it in the future you can get the one peice tub out and a new one back in without having to do major demolition. 

I would wire the house so each of the rooms has a phone and TV hookup in it, in the bigger rooms I'd even think about putting two in. 

Three way switches for any room with more than one entrance.  Also on the same note I would add the extra wiring and put in big enough switch boxes so that in the main rooms you can put in ceiling fans and control both the fan and the lights with seperate wall switches. 

In each room I would put in at least one empty outlet box with conduit running to the basement so down the road you can add a connection for whatever you want without lots of work.