To stand up to the horizontal force of wind, skyscrapers need the right combination of stability and flexibility. They have to be rigid enough that the wind can't push them too far from side to side, but flexible enough that they can give a little, absorbing some of the wind energy.
The WTC crew ran extensive tests to find out just how much sway they could allow without disturbing the building occupants. They put structural models in wind tunnels and even lured unsuspecting test subjects to movable rooms hooked up to heavy hydraulics.
In the end, they designed the towers so they could sway about 3 feet in either direction. To minimize the sway sensation, they installed about 10,000 visco-elastic dampers between support columns and floor trusses throughout the building. The special visco-elastic material in these dampers could move somewhat, but it would snap back to its original shape. In other words, it could give a little and then return to its initial position, absorbing much of the shock of the building's swaying motion.
In addition to the support structure of the buildings, the WTC crew had to consider how people would actually get around the towers. Elevator systems have always been a difficult balancing act for skyscraper designers. As you build upward, increasing the available space and therefore occupancy of a building, you need more elevators to handle the extra people. But adding more elevators running to the top floor reduces the available floor space somewhat, and therefore total occupancy (which reduces the revenue potential). It's tricky getting all the numbers to work out, and it functionally limits the size of the skyscraper. Before the WTC, architects were hesitant to build higher than 80 stories, largely due to the elevator problem.
The WTC crew proposed a completely different system for the huge towers. Instead of building enough elevators to move everybody from the ground floor to their destination, they decided to split the trip to the upper floors between multiple elevators. If people wanted to get from the ground to the top floor, they would need to jump from elevator to elevator, in the same way you might switch cars on a subway system.
First, they would take an express elevator from the main lobby directly to a sky-lobby on the 78th floor. From there, they could go to their destination floor directly. To keep things orderly, all the 55-person elevators had doors on each side -- you would enter on one side, move to the front, and exit on the other side. This way, the passengers could keep their place in line all the way up.
Essentially, each tower functioned as three buildings stacked on top of one another. The system turned out to be a great success -- with 99 elevators total per tower, each serving only specific floors, occupants could get around quickly and easily. Most super skyscrapers built after the WTC used the same basic system.