It's not uncommon for videogame sound effects to be sourced from sound effect libraries, which is why you sometimes hear the same ones show up in movies and TV shows. I've heard the whooshy Doom door sound effect in Doctor Who, Event Horizon, Galaxy Quest, and plenty of other places. But there is one specific bird sound, a tremolo warble that I know from Age of Empires, which I seem to hear more than anything else.
Mostly it's in pop songs. It plays repeatedly over the outro of Anaconda by Nicki Minaj, and you can hear it in Babylon by Lady Gaga. It's in Pacific State by 808 State and Animals Beat by Skrillex. It's in multiple tracks by Aphex Twin. I think it's in Michael Jackson's Thriller, but that might be a different sample of the same call, and I'm halfway convinced it's been used in heavily processed form in Lana Del Rey's Million Dollar Man. According to Who Sampled, it's in at least 190(!) tracks. Basically, anywhere someone wants things to sound a bit wild and maybe like you're in the jungle, this is the go-to bird cry.