Personally, the final battle with The Boss, when the music came in and kept slowly building, that was just one of the single greatest moments in gaming, period. The End was also amazing. It looks like just about every boss made the list, which is just an amazing testament to the amzing quality of these games, every boss but Fat Man anyway, but I really can't blame them for leaving him out.

Wait...ocelot is the son of the Boss and the Sorrow?! How did I miss that? Did they revel that in Portable Ops?