On Frasier, particularly seasons 8-10, there are a number of instances where a character will ask another 'Why'd you do it?' in an exaggerated fashion. Martin asks Niles when he leaves Eddie in a kennel, and asks Frasier when he throws dancing Santa off the balcony. Noel asks Frasier when he doesn't uphold a deal to get Scott Bakula's autograph. There are a couple others, and they all say it the same way! What is the origin and significance of this line and delivery?
I'm pretty sure this is a reference to the song "Why'd You Do It?" by Marianne Faithfull. The inflection on "do" is exactly the same as Faithfull's.
Here's a link to the song on YouTube, but be aware the lyrics are NSFW.