Now of all the MGS games Id say the first one had the best plot. MGS2 was a bit strange, MGS3 was cool and all but was in the past and MGS4 was too epic and confusing at some stages. MGS1 got it just right.

And I always loved the plot in Final Fantasy VIII, even though not many FF fans rate it highly.

I Have No Mouth and I Must Scream for the PC years ago had a very chilling plot in my opinion.

Doki Doki Majo Shinpan.

NO!

I agree on the Jak games because it really was an interesting story unlike the common technique of throwing a bunch of garbage into the mix about the world should become filled with tree huggers and befriend everyone

either that or Majoras Mask

+1. Still feels like the early Suikoden's really got jumped in notoriety. Also Chrono Trigger and Lunar 1&2.

Fear

1. Legend of Zelda Orcarina of Time
the ending and travelling through time was epic.
2. Metroid prime series
okay, this one is hard to figure out, but watching Dark Samus' plan crumble, and resurface stronger was great to me.
3. Fire Emblem (PoR, than RD)
this greatly deep story was filled with exellent characters and great plot twists (i.e. whaa? Bengion vs. Laguz the whole time?)
4. bioshock
just a great story all around (whould you kindly?) along with the story of rapture's rise and fall the whole time
5. Armored Core: For Answer
wile the ORCA and Collared storylines were decent, the path where you team up with Old King and destroy one of the Cradles, killing 100,000,000 people was very dark and great.
(SUPER EDIT) i also loved the character development of Old King, Otsdarva (the most complex character yet, changing between Otsdarva of Collard and Thermidor of ORCA) and White Glint
6. Fallout 3
for characters liek John Henry Eden, Gary, and Liberty Prime

Chrono Trigger-Cross

I agree with "The World Ends With You." Sure, there were only 4 playable characters (and only two were in battle at one time), the game spans for 21 + 1 days and is all set in Shibuya, but that game proved that less does not necessarily mean worse.

In my opinion, the Boktai series (GBA + DS) and Mother 3 have the best storylines.

(By the way, I was checking this article for a good game to buy. I am considering "Final Fantasy X," yet that would have to come after "Retro Game Challenge." You know why...)

TWEWY would get my nomination for recent times, I found myself always desperate to find out more about what was really going on. Couple that with wonderful art style and tension raised by playing with characters you dont fully trust and battling other characters you feel could be fantastic partners for you was something I hadn't experienced in a game before.