Square Taper
This is currently the most popular design by far. This interface consists of a spindle with square tapered ends which fit into square tapered holes in each crank. Tightening the two together creates a relatively efficient and simple interface.
OctalinkThis system was designed by Shimano. The Octalink system provided a greater contact area between crank and spindle, so it had a stiffer interface. Octalink exists in the marketplace in two variants, Octalink v1 and Octalink v2. The difference between the two can be seen by the depth of mounting grooves on the bottom bracket spindle. XTR, 105, Ultegra 6500 and Dura Ace 7700 cranksets mate to version one bottom brackets, while more recent mountain bike designs use the deeper-grooved version two. The system is proprietary and protected by Shimano patents and licence fees, thus relatively few companies aside from Shimano produce Octalink cranksets. Many competitors have adopted the square taper and ISIS designs as an alternative. In use, Octalink has been shown to loosen because it is not a taper-fit but merely a tight spline fit. Reverse torque loads can cause the crank bolt to undo, and the crank can be irreparably damaged if this is not checked.
ISIS Drive
Outboard / External Bearing
Many current designs are now using an integrated bottom bracket with outboard bearings. This is an attempt to address several issues associated with weight and stiffness. Because of the relatively small 1.37" (36 mm for shells threaded to the Italian standard) diameter shell, designs that place the bearings inside the shell can either have large bearings and a thinner spindle, which lacks stiffness, or smaller bearings and a thicker spindle (such as the original Shimano Octalink), which is stiff but less durable. External bearings allow for a large diameter (hence stiff) and hollow (hence light) bottom bracket spindle. They also offer more distance between the two bearing surfaces which contributes to stiffness while allowing lighter components.source: http://en.wikipedia.org/wiki/Bottom_bracket