I also, can't to this day say Fate Stay/Night could realistically make the cut into my top anime list. Yet its been in there on my sig, when I could think of many more deserving series that could take its place.
It just had too many flaws and Shinji's character in the anime was so damned annoying.
I never played the game or saw anything outside the anime though, and I'm still a rabid fan regardless.
My conclusion: Saber, Rin, and Rider.
EDIT: Haha, I called Shirou Shinji. Thats how annoying he was. -_-