Why is Beethoven's "Ode to Joy" so prevalent in anime? 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?
With "Read Or Die", it was part of the plot, since they cloned Beethoven himself. With most of the other instances, it's selected background music, and I'm not sure I'd say it's even that prevalent. Schubert's Ave Maria is used in a lot of shows. Same with Erik Satie's Gymnopédie No.1, Beethoven's Moonlight Sonata or Pathetique, Pachelbel's Canon in D, Ravel's Bolero, or what about Handel's Messiah?

Aside from the obvious thematic reasons you'd want to pick a classical piece, especially in shows that are set in a classical setting or at a music school (Nodame Cantabile, La Corda, etc), sometimes the animation/scene/sequence is storyboarded/tailored for a particular piece of music. In Evangelion, you had that super long pause during Ode to Joy. In Legends of the Galactic Heroes "My Conquest of the Sea of Stars", there's is a beyond epic 15+ minute long space battle that is intricately choreographed to the entirety of Ravel's Bolero.

Oddly, while it's said that Vivaldi's Four Seasons is the most played classical piece ever, I don't think it's used in anime all that much.

There's a thread on ANN that lists some of the more common classical pieces that get used in anime.