When Fluttershy is crying over Philomena turning to ash, her whimpering sounds are her squeaky "I'm Fluttershy" from when she first met Twilight in "Friendship is Magic, part 1".
Fluttershy and Hummingway briefly vocalize the theme song.
When Pinkie eats a cake meant for Celestia, Mrs. Cake's gasping is Pinkie's prolonged gasp from "Friendship is Magic, part 1" when she first saw Twilight.
Friendship Report: Fluttershy learned not to jump right to conclusions without asking for advice.
The title is a spoof of the phrase 'a bird in the hand is worth two in the bush'. The saying itself means a sure thing is preferable to the mere chance at something more.