thewayneiac: Crow calls are often used in anime to question the characters' intelligence, but I doubt if that's the case here. (Crows are said by the Japanese to cry "Aho!" = "Idiot".)
Shin-seiki: There are sound effects that go with certain situations in an almost clichéd way; in NGE, crows cawing go with sunsets (see the end of #10, the Asuka/Hikari scene in #18, and the sandbox scene in #26', among other examples).
