Beethoven's "Ode to Joy" is an important song in Evangelion.
The song is also important to the Read Or Die OVA.
And in the 13th episode of Gunslinger Girl, the girls start watching a meteor shower and want to listen to this particular as background music.
Why is this particular song so prevalent in anime? It may be a well-known piece, but there are lots of other well-known pieces of classical music.
According to Wikipedia, the song is played during Japanese New Year's celebrations. That would explain something, but in none of the above examples was there a New Year's celebration.
So, why does anime feature this particular song more heavily than other classical pieces?