Bikes are designed in different proportions. Some manufactures bikes are longer for a given frame size.

The micro-style frame, popular these days (eg Giant) uses a lowered top tube with more clearance, but retains the top tube length of a standard style frame.

You need about 1-2" clearance on a standard frame, but given that, then length (top tube+ stem) is the most important factor for fit.

The length you need depends on your size and your riding style. Riders who can get low for aerodynamic drag need a longer frame. The bike company Serotta have a fitting system which is a little less naive than some of the others. They also make great frames, but you dont need to buy one to use their system.