I was struggling with the fifth one, but the rest one were easy picks.
5.- Roy Campbell: while probably not the most competent chief to bring in a mission (he might drop you some bomb truths halfway through you might not like much), he's nonetheless a loyal companion, one that has successfully guided Solid Snake through two impossible operations and made him live to tell the tale. He went extra lenghts to protect the people he cared, even if it meant earning the spite of everyone else. He's one of the very few characters that close his arc story happily, and given everything he has went through, it's kind of amazing at that point.
4.- Ocelot/Revolver Ocelot/Liquid Ocelot/Shalashaska: the man who has starred in most games of the franchise, I'd presume. The nexus between all the vital plot points in many, while being a sadistical charmer in all of them. If I have to pick, his awkward younger self was his best incarnation.
3.- Raiden/Jack the Ripper: the misunderstood main character from MGS2 takes the third place not only because who he is, but what he represented. It's a real shame that later retcons totally tried to erase what he stands for in the first place, but the fact that I massively enjoyed Revengeance makes me push to put him here; because no matter how much the later games tried changing the past, the past always remains unchanged.
2.- Hal "Otacon" Emmerich: A character that seemingly never gets too much credit. Otacon is probably the most pure of heroes in this whole franchise, and what he pales in comparison to the likes of Snake, Raiden or Big Boss, he makes it up in wittiness, courage (yeah you read that right) and good-willed intentions. He manages to bury his father's legacy while helping Snake bury his, he manages to erase The Patriots in the collective effort with Sunny and the rest of military forces, and while it really sucks that his arc is concluded by never having a truly happy ending, he nonetheless stucks with Snake and Sunny until the rest of their days.
1.- Solid Snake: is there really anything to add here? Solid Snake, the flawed likeable baddass from this franchise. The man who probably endures the most throughout his "short" lifespawn, and never ever complains or go batshit insane like his father did. The man who was self-conscious about what he had become, and the man who even when being an old geezer went one final time to end everything. You don't get cooler than that.