A good story needs a great leader and there are many in the world of science fiction be it in cartoons movies or comics. One of the greatest fictional leaders of all time has to be Optimus Prime from the Transformers series. Optimus transforms from a truck into a robot and is one of the most courageous and formidable opponents for the Decepticons to face. Optimus always makes the right decisions often choosing to go into battle and take on the big guns. He's a leader who leads from the front which has often meant getting himslef killed. In the recent IDW comics Optimus leaves leadership to Bumblebee which has been a strange twist in the series.
Emperor Palpatine in the Star Wars saga has to be one if not the greatest leaders in the Galaxy. He took control of the Republic and turned it into an Empire that no one wanted to mess with. Palpatine knew how to delegate giving his regional governors control of their star systems. He also provided his officers and commanders with a strong space fleet and a planet destroying Death Star so he obviously believes in the right tools for the job. Palpatine led a very secretive organisation and only shared information when it was necessary. He was a master strategist and he will be missed.
Cyclops from the X-Men is a great leader in the comics but not so much in the movies. Cyclops AKA Scott Summers is an all action leader who knows how to get things done and always leads from the front. He has years of experience leading the X-Men and dealing with unruly members of staff such as Logan and in his career he has seen many strange things and was even merged with Apocalypse at one point. It helps that Scott has a telepath girlfriend at his side constantly to help him out. He's cool with inter work relationships it would seem.
Captain Picard from Star Trek is another fantastic leader. During his career as captain of the Starship Enterprise he was involved in numerous battles and diplomatic wrangles. He is a cunning leader with great debating and diplomatic skills as well as excellent hygiene. His catch phrase is 'Make it So' and when it is uttered his crew never hesitate. Picard was at one point assimilated with Borg, a nasty group of cyborgs who assimilated anything they could get their hands on. Picard did regain his humanity but was left emotionally scarred by the incident.