In general terms:
Sidewinder- the motor is in line with or parallel with the spinning blade. Generally it spins a little faster, around 6000 RPM and is more popular among finish carpenters and general contractors. Typically, the blade on most of these is on the right hand side of the saw, often referred to as a right handed saw.
Worm drive- the motor is in the back of the saw perpendicular, or at a 90 degree angle to the spinning blade. It may spin slightly slower than a comparable sidewinder but has more torque or power. The saw also tends to be longer and heavier. These saws are preferred by most framing carpenters and deck builders. On most worm drive saws, the blade is on the left hand side of the saw, and often referred to as a left handed saw.
As for which is "better", it depends on the application, as well as the user. Both designs have positives, negatives and tradeoffs. Many carpenters will have both in their arsenal.