The song is basically symbolic of Tomoya's feelings about Nagisa over the entire series. In the first season, it's adorable and twee. In the second half of the second series, it is heartrendingly sad (especially when Tomoya sings it to Ushio). And at the end, it comes back, with the whole family singing it together, as...
~After Story~'s OP song, "Toki wo Kizamu Uta", counts as a Heartwarming Moment. Directly translated, it means "The Song That Transcends Time," which, put in context, is perfectly symbolic of Tomoya's love for Nagisa.
The lyrics are absolutely heartrending when placed in context with the series:
"It was only you who I loved, It's a song I only sang with you, It's the time we passed together, I can't go on all alone."
"Nagisa's Theme". Dango Daikazoku without its vocals but it has a beauty of its own.
"Nagisa Warm Theme Piano" is possibly one of the most heartwarming themes on Clannad. When Tomoya finally meets Nagisa and decides that meeting her was the best thing that could have happened in his life this music is the best. It depicts quite well the love of Tomoya toward Nagisa.
"Town, Flow of Time, People" plays whenever something sudden or amazing is happening; which means it plays at many of the greatest moments. A worthy song for it, too. Sometimes specifically starts at around 1:45 to maximize the music's impact.