Any moment in Clannad or Clannad AS that was supposed to make you emotional.They mastered that.The saddest three would definitely be Nagisa's,and Ushio's deaths,followed very closely by where everyone forgets Fuko.
Another given is the moment where Momiji tells Tohru about his mom.From all the comedy in Fruits Basket,this one hit me hard.Poor Momiji!!
Also when Shion almost dies from No.6.I love Shion and after the trouble Nezumi went to save him so many times,he couldn't die.And I wouldn'tget any romantic payout if he did.
Other scatterd momets here and there got to me,but these are the most memorable and profound.