I knew that CLANNAD was going to get a moment in this list. The question was: which one? I ended up settling on the last real complete and independent story arc for the show in 2008 besides Nagisa’s: Kotomi’s arc, the core of which spanned episodes 13 and 14 of the first series.
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I don’t know if it’s because of the character of Kotomi and how innocent (and clueless and freakin brilliant) she is or the fact the two characters that I like better – Kyou and Tomoyo – didn’t get “real” story arcs (though Tomoyo got more of one than Kyou), but Kotomi’s arc seemed to be the best story arc in the series to me so far – After Story included.
There may be short moments here and there that may be very good as well, but it seemed like that these two episodes were perhaps the best pair of episodes in CLANNAD, at least thus far. That earns them a spot in the 12 Moments of Anime.
The 12 Moments of Anime project is the brainchild of CCY.

I should say that the concluding episodes of Sunohara’s arc does give these two episodes a run for it’s money, though.
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Kyou deserves own OVA! lol..
Anyway, Kotomi’s arc was not such a big deal for me for some reason..
I might say that it’s the weakest arc..(sorry)