The fuel cell controller is needed to get the Highwayman at The Den's Junkyard working.
You can find it with Skeeter at Gecko's Junkyard. You trade a Super tool kit for it (reward from the quest Deliver pliers (tools) and a wrench to Valerie). Alternatively, you can pickpocket it from Skeeter (impossible after the patch), or simply just kill him.
- If you cause the Gecko Reactor to melt down and leave the city prior to collecting the fuel cell controller, you will be unable to obtain it without the use of an inventory editor.