I suppose I'll say what the best plot-driven animes I've watched <2002 and >2007: (I'm more into romances than other genres so you'll see me biased towards those)
<2002:
Crest of the Stars
Vandread
Martian Successor Nadesico
Fruits Basket
Noir
Cowboy Bebop
Angelic Layer
Haibane Renmei
Rurouni Kenshin + OVAs
Hoshi no Koe - Best romance I saw within a movie's timeframe
Onegai Teacher
Hunter x Hunter
Slayers + Next and Try
Princess Tutu - For a mahou shoujo the story pleasently surprised me
>2007:
Clannad - This is the only anime that made me CRY. And by cry I don't just mean 'eyes tear up'.
Tengen Toppa Gurren Lagann - I think this came out in 2007... Anyway, a must watch. Ever wonder how strong you can get just by being AWESOME?
Macross Frontier
Higurashi no Naku Koro ni + Kai and Rei
Kaiba - it looks weird, but trust me it's really good
True Tears - seconded
Toradora!
Bakemonogatari
Code Geass - if you love...
Death Note - .... anti-heroes
Nana
Toki wo Kakeru Shoujo
Gundam 00
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