FADTEFGWF
ZENITH. GET. OUT. OF. MY. HEAD.
Besides those three, I have to add in a few here...
Persona 4- Some may argue that the tale is farfetched, but all of the elements end up being so wonderfully meshed together and the psychological standpoints of the characters REALLY help to make this a brilliant story that made me sob my heart out at the end.
Persona: Trinity Soul- I KNOW ANOTHER PERSONA TITLE SHUSH. Again, it is VERY psychologically oriented, and although graphic and scarring at times, a good set of artwork SHOULD do that. Everything adds up very smoothly at the end and just is...marvelous. Another tear-jerker.
Rurouni Kenshin- Ah, a beautifully handled, semi-historical anime! There are very very few historical pieces out there, and I think this one hit it. I have yet to see another historical anime that comes anywhere near close to the realisticness that RuroKen. Again, the characters are deeper than we originally see them as the story progresses, and character development is a MUST if you want a good storyline.
Yu-Yu Hakusho- Say all you want, DBZ fans, but most of the show is screaming and powering up, better known as filler. The storyline is near non-existent; they're just trying to save the world yadda yadda from the evil aliens. Yu-Yu definitely seems to be the top fighting anime I have seen; while on the surface it may seem that it's just a save-the-world thing, again, the characters make the story. It's not just black and white. The 'villians' have actual motives for their goals, some that actually make us sympathize with the villian at times (See: Dark Tournament), the good guys can borderline seem like badguys, and the ending was actually one that was absolutely fitting for it.
Pokemon the Movie 2000- SHADDUP I THINK IT WAS PRETTY GOOD.
Metroid Prime (original)- There is something to say about a game with absolutely no dialogue, and can yet still tell a great story via optional log scans. It's an adventure game, but you can totally pick out the story as to what happened, how it happened, and why it happened. It's a VERY difficult thing to achieve in any game format without dialogue, ESPECIALLY an FPS.
I can't think of any more right now, but yeah those are some of my most favorite storylines ever.