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There are lots of options for controllers, but honestly it makes little difference as the all function similiarly. The choices come down to how much power they can handle, and what options, such as cruise control and regen, they have.
Power on a stock controller is a function of the number of fets they have. Given in multiples of 3, the more fets a controller has the more power is it can handle. For example, a 6 fet controller can do substantially less than a 9, 12, or 18 fet controller. Upgrades can be made such as beefing up the traces and upgrading to higher quality fets, but it's almost always cheaper and easier to just upgrade the controller.
 Lyen controllers from ebike sized to motorcycle sized
As of 2011 there are two controllers that are programmable via USB - these are the popular controllers made with Infenion chips (and copies of Infenion chips) and Kelly. The Infenion controllers aren't a made by anyone company, but all use the same series of Infenion micro controllers. Most (but not all!) controllers sold by major retailers are Infenion, and can be easily modded to re-program. Please see my page on programming for more info.
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