A lot of anime I have seen use cherry blossoms, especially when they fall from the sky. Romantic or emotional scenes have cherry blossom in the background. In many anime, there is a childhood scene in which friends see cherry blossoms falling and remember that day forever or they meet their love when the blossoms are falling.
Why is it always cherry blossoms? Does it have a special significance in Japanese culture?
Cherry blossoms are very prominent in Japanese culture. From Wikipedia:
In Japan, cherry blossoms also symbolize clouds due to their nature of blooming en masse, besides being an enduring metaphor for the ephemeral nature of life, an aspect of Japanese cultural tradition that is often associated with Buddhistic influence, and which is embodied in the concept of mono no aware. The association of the cherry blossom with mono no aware1 dates back to 18th-century scholar Motoori Norinaga. The transience of the blossoms, the extreme beauty and quick death, has often been associated with mortality; for this reason, cherry blossoms are richly symbolic, and have been utilized often in Japanese art, manga, anime, and film, as well as at musical performances for ambient effect. There is at least one popular folk song, originally meant for the shakuhachi (bamboo flute), titled "Sakura", and several pop songs. The flower is also represented on all manner of consumer goods in Japan, including kimono, stationery, and dishware.
1 Mono no aware (物の哀れ) [...] is a Japanese term for the awareness of impermanence (無常 mujō), or transience of things, and a gentle sadness (or wistfulness) at their passing.
So yes, they do have a special significance.
Hanami (lit. "flower viewing") being one of the nation-wide festivals would help.
Note that the school year starts in April (graduation in late March), while depending on the location, cherry blossoms are prevalent from the end of March to early May.
Everyone knows romance is all about love at first sight on the first day of school and confessions during the graduation ceremony, right?
TvTropes' Cherry Blossoms article could be an interesting read, on top of Wikipedia's.
