Cowboy Bebop (1998)
[SPOILER="Spoiler"]
[Image: http://www.romston.com/wp-posts/10-01-17-CbSC/cb003_675_518.png]
[/SPOILER]Inuyasha (2000)
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[Image: http://2.bp.blogspot.com/_9xZXVskUTpk/TI_jNMCkERI/AAAAAAAABok/zYaCPPMWCaI/s1600/inuyasha-screenshot-tv-004-0214.jpg]
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Gundam 0083: Stardust Memory (1991)
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[Image: http://3.bp.blogspot.com/_mwyHgbVMknw/TD8uxSY4PsI/AAAAAAAAAwo/M6CSRbODZNA/s1600/gundam+0083+screenshot+2.png]
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MD Geist (1986)
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[Image: http://screenshotcomparison.com/images/DBNL_2981536704.png]
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Fullmetal Alchemist (2003)
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[Image: http://www.animeshinobi.com/wordpress/wp-content/uploads/2006/11/fullmetal_alchemist8.jpg]
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New:
Lucky Star (2007)
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[Image: http://blog.jpopdb.org/media/anime/lucky_star/lc_24_03.jpg]
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Fullmetal Alchemist: Brotherhood (2009)
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[Image: http://thenullset.files.wordpress.com/2009/08/summer259901.jpg]
[/SPOILER]Gundam Unicorn (2010)
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[Image: http://www.linearseat.com/wp-content/uploads/2010/11/DeltaPlus1.jpg]
[/SPOILER]Steins;gate (2011)
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[Image: https://blogs.emory.edu/animec/files/2011/05/steins-gate-06-08.jpg]
[/SPOILER]KissxSis (2010)
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[Image: http://www.myanime.me/screenshots/KissxSis-episode-1-screenshot-006.jpg]
[/SPOILER]I also think atmosphere and budget can have a lot to do with it, but, when I look at Fullmetal Alchemist vs Brotherhood, or Gundam 0083 vs Gundam Unicorn, I just feel like the older style looks a lot better. The budget difference between each of the two would probably be about the same, and they're each of the same type (TV vs TV anime, OVA vs OVA) so I feel the comparison is fair.
So, which do you prefer?