There are lots of different ECU's on the market. DTA, Emerald, OMEX, Megasquirt (probably one of the cheapest) etc. An after market ECU is something you can have mapped to suit the engine you have, for instance if you put cams, throttle bodies etc on a lets say Zetec engine, the standard ECU and Map are no good for it because the fueling etc doesn't match up anymore, so you get an aftermarket one and have it mapped to your engine. (Expensive though)