Final Fantasy - IX without question. Has the best story,characters and setting in the series, and one of the best villains and soundtracks. The visual style is also my favourite in the entire series.
Metal Gear Solid - MGS3. The strongest story in the series, with the most interesting setting and gameplay elements. Also lacked most of the more eccentric plot elements of the rest of the games in the series, perhaps because it had the advantage of being chronologically the first game in the series.
Dark Souls - Dark Souls 1. I have yet to play III, so who knows if this will change at some point, but right now I still hold the first Dark Souls as the best in the series.
Mega Man - 4, perhaps mostly due to nostalgia, although i can still go back and play the game pretty much whenever. It also introduced the mega buster to the series. Very close call between this and 2.
