Well traditionally, manual transmission is still best on gas mileage. However these days, we're beginning to see some newer cars with automatics that have an EPA rating of only 1 or 2 MPG less than the same model car equipped with the manual. So small, but they've gone more efficient. SOME vehicles get better mileage (5 mpg or more) as an automatic compared to the manual. This kind of example can be reflected in the Toyota's like the RAV4, and the FJ Cruiser.
For manual tranny, the driver controls when to shift gears. In an automatic, the gears shift automatically (no surprise there) when the RPMs reach a certain level. The RPMs seem to run high before the car shifts gears, much higher than you would let them get with a standard transmission. When they run high, the car burns more gas which result in reduced gas mileage as compared to manual transmissions. It's just a basic theory, but now with all these hybrids, electric, and fuel cell vehicles out, gas mileage no longer mean anything anymore.