Top 3 VG plots from each gaming era.

[Wolf Kanno]

Basically list your top 3 video game stories from each gaming generation. You only need to go back as far as you desire and the only stipulation is time frame. If you're going back to the 90s, start in 90-94, then 95-99, then 2000-04 and so forth. Just try to keep it within an adequate time frame that is not too short or too long. I'm doing a bit of research into a pet theory of mine.

Obviously you are not limited by genre or gaming device so have fun.

[Bolivar]

8th Generation

The Witcher 3: Wild Hunt
The Order 1886
Call of Duty: Ghosts

7th Generation

The Last of Us
Heavy Rain
Assassin's Creed II

6th Generation

Metal Gear Solid 3: Snake Eater
Final Fantasy X
Legacy of Kain: Defiance

5th Generation

Final Fantasy VII
Xenogears
Metal Gear Solid

4th Generation

Tactics Ogre: Let Us Cling Together
Dragon Quest V
Chrono Trigger

3rd Generation

Dragon Quest IV
Final Fantasy II
Tetris!

[Ayen]

3rd Generation
Ninja Gaiden
Ninja Gaiden II
Ninja Giaden III

4th Generation
Comix Zone
Final Fantasy VI
Mortal Kombat II

5th Generation
Final Fantasy VIII
Metal Gear Solid
Resident Evil

6th Generation
Devil May Cry 3
Final Fantasy X
Metal Gear Solid 2

7th Generation
The Last of Us
The Walking Dead Season One
The Wolf Among Us

I haven't played many games in the 8th Generation so can't say.

[Vermachtnis]

3th
Ys I & II (Grafx-16) [It's one game that had to be seperated due to limitations.]
Dragon Quest III (NES)
Final Fantasy II (NES)

4th
Phantasy Star IV (Genesis)
Final Fantasy VI (SNes)
Chrono Trigger (SNes)

5th
Final Fantasy IX (PS)
Persona 2 (PS)
Xenogears (PS)

6th
Legend of Zelda: Wind Waker (Gamecube)
Phantom Brave (PS2)
Yggdra Union: We'll Never Fight Alone (GBA)

7th
Growlanser: Wayfarer of Time (PSP)
Dark Souls (PS3)
Xenoblade (Wii)

8th It's still going, buuuuut...
Senran Kagura: Burst (3DS) Good "plot" in all sense of the word.
Gravity Rush (Vita) The game itself's plot isn't all there, but the foundation is. It feels very episode one-ish and it could really go somewhere.
Persona 4 Golden (Vita)

[Pheesh]

7th Gen
Last of Us
Bioshock: Infinite
Mass Effect 2

6th Gen
Final Fantasy X
Kingdom Hearts
Star Wars: Knights of the Old Republic

5th Gen
Diablo 2
Final Fantasy VIII
Metal Gear Solid

[Bright Shield]

The lack of Suikoden II makes me sad.

[Wolf Kanno]

The lack of Suikoden II makes me sad.

You could always do your own and rectify this.

3rd Generation:
Final Fantasy III
Leisure Suit Larry in the Land of the Lounge Lizards
Dragon Quest III

4th Generation
Final Fantasy VI
Chrono Trigger
Final Fantasy IV

5th Generation
Xenogears
Metal Gear Solid
Final Fantasy Tactics

6th Generation
Persona 3: FES
Metal Gear Solid 3: Snake Eater
Shadow of the Colossus

7th Generation
Portal
Catherine
Journey

[Forsaken Lover]

5th Generation
Xenogears
Metal Gear Solid
Final Fantasy VII

6th Generation
Metal Gear Solid 2: Sons of Liberty
Final Fantasy XII
Legacy of Kain: Defiance

7th Generation
Mass Effect 2
Heavy Rain (the story itself isn't the best but dat presentation)
And I don't have a third one.

[Carl the Llama]

Hope you don't mind, I cba to look up generations and ect, I'm just going to list my top 3 per console if that's ok:

SNES
Chrono Trigger
Final Fantasy IV
Final Fantasy V

Nintendo 64
Zelda: Ocarina of Time
Zelda: Majoras Mask

Playstation
Lunar: Silver Star Story Complete
Breath of Fire IV
Final Fantasy VII

Dreamcast
Skies of Arcadia
Grandia II

PS2
Persona 4
Final Fantasy X-2
Metal Gear Solid III

XBOX
Fable: The Lost Chapters

PS3
The Last of Us
Metal Gear Solid IV
Uncharted II

The PS2 list could have been a LOT longer... but 3 games is the rule so.

[Randy]

4th gen
FF6
FF4
Chrono Trigger

5th gen
Chrono Cross
FF9
FF7

6th gen
FF10
MGS3
Shadow Of Colossus

7th gen
Mass Effect 1
Xenoblade Chronicles
To The Moon

[Colonel Angus]

2nd Generation
Centipede
Frogger
Ms. Pac-Man

3rd Generation
Final Fantasy II
Castlevania III: Dracula's Curse
Super Mario Bros. 2

4th Generation
Final Fantasy VI
Chrono Trigger
Phantasy Star IV

5th Generation
Final Fantasy Tactics
Chrono Cross
Castlevania: Symphony of the Night

6th Generation
Final Fantasy XII
Final Fantasy X
Dragon Quest VIII

[Loony BoB]

1990 1989-94
Final Fantasy VI - SNES, 1994
Prince of Persia - PC, 1989
Solar Winds - PC, 1993

1995-99
The Longest Journey - PC, 1999
Final Fantasy VII - PSX, 1997
Grandia - PSX, 1997

2000-04
Final Fantasy IX - PSX, 2000
Final Fantasy X - PS2, 2001 (I don't like the lead characters but I appreciate the plot)
Final Fantasy XI - PC, 2002 (what little I've played, it's already right up there)

2005-09
Dreamfall: The Longest Journey - PC, 2006
Lost Odyssey - 360, 2007 (haven't finished it but it's easily one of the best plots regardless)
Mass Effect Trilogy - 360, 2007 (using the first game to represent the trilogy)

2009-14
Journey - PS3, 2012
Deus Ex: Human Revolution - PS3, 2012
Gone Home - PC, 2013 (likely the most underrated game on this post)

There are a lot of games I haven't played and are confident would make the list if I had played them, but hey, can only go by what I know. Also, it's hard to really split plot and story. Some of the games I've played have a really cool plot but poor story, and vice versa. Plot, for me, is the over-arching concept of what is going on, while the story is how it actually plays out. A great example of a good plot but poor story for me would be Warzone 2100, and a good example of a very basic plot but a good story would be the Uncharted series or Dwarf Fortress.