We tend to go with the Touring Plan's crowd calendar first, choosing which parks on which days. Then we book dining next, based on which park we will be in. If there is a restaurant we really want and it doesn't fit our original schedule, we tweak with it or park hop.
After that all bets are off - we usually go for a week, so we hit MK at least twice, Epcot at least twice, and the other two at least once. Then we double back and see shows, play mini-golf, swim, or visit a resort or two. We are also big fans of early mornings in the parks and mid-day breaks - it's amazing how much you can get done in the first two hours.
I'm also one of those obsessive-spread-sheet people who puts everything down before we go, but mostly that's just to ramp up my excitement (and keep track of reservation numbers!).