KoF '97, kind of surprised that got a few votes
I voted for KoF '97; this is the first time that I have taken part in such a poll, so I took some time thinking about it. The reasoning for my choice has to do with the storyline elements and the effect they produced.
KoF '97 represented the climax of the Orochi plot, which was an interesting twist on a piece of ancient Japanese folklore. I found that in itself to be very creative in itself, but this was taken to a higher level by the way the game presented the story. It created dynamic characters that actually changed as the game went along, specifically the Orochi versions of Iori, Leona, and the New Face Team.
The idea of alternate characters was a relatively new concept at the time (the only thing I could think of that appeared around that time was "Evil Ryu" from the Street Fighter series,) but it was beautifully executed. I have praised this aspect before and, as another member of this board pointed out, that' idea is something that stays with you; to paraphrase what he says, one cannot forget Leona's bloodlusting scream from that game. In short, the game didn't just tell you what you should know through cinematic cutscenes, it made special characters, backgrounds, music and other effects just to make it so substantial that you carry the experience with you out of the arcade.
It's sort of strange evaluating an action game based on its storyline. As one famous developer (John Carmack of Quake fame) said, stories are as important to games as they are to porn movies; you expect them to be there, but it's not a big deal. However, one of SNK's star qualities is to create a plot and made it important. Any game can essentially be condensed into a numbers and formulae; perform the right sequence of moves in the right situation (aka combos) and you will move on to the next stage. However, when you give these elements a name, a personality, loves and hates, goals and ambitions, then you have succeeded in making characters that interest people and draw them to the game. There is no doubt in my mind that this is SNK's greatest strength, which is why there are posts in this forum discussing these fictional people that players seem to care a great deal about.
It comes down to the simple concept that any game of the genre could either be a space monkey chore of pressing buttons in a set order or an unique fighting experience with blood and sweat and fire coming out of your hands. The KoF series focusses on making players feel the latter, despite using relatively old technology. KoF '97, despite all its limitations, is my favorite example of that quality, thus my vote.