The Nagisa/After Story route in Clannad is one of the few visual novel moments that hit me right in the feels. Definitely an experience i wont forget anytime soon.
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Another honorable mention i would like to add, is Saya no Uta. Now, whilst it most certainly is different from Clannad in terms of content and story, it left a similar impression on me. The endings in particular were both sad/bittersweet and impactful, contrasting well with it's rather dark and macabre themes, which i loved. That, coupled with great writing and an excellent soundtrack makes it one of the best Visual Novels i have had the pleasure of reading.