Yeah, according to a quiz on this site Boober was named after a mad cow. Here's some others I've looked into, I can't say for definite that they're right but though
Boober - angry cow
Gobo - a piece of metal or similar with a pattern cut in it for use in stage lighting and projection.
Henchy - taken from Henchman
Balsam and Gillis (and possibly Feenie with the spelling changed) - cast and crew members' surnames.
Red - um, well, she wears a red sweater.
Wembley - Wembley Stadium
Herkimer - county of New York
Merkey (Merggle) - taken from 'murky', description often applied to water.
Mermer (Merggle) - possibly taken from 'murmur' but also a sort of distortion of 'mermaid'
Pedley - is a place in California
Phil Fraggle - is voiced by Phil Balsam
Cantus - to sing (in Latin)
Brio - lively, with vigour musical term con brio
Brool - discussion over at FR.com seems to have settled on it being like a roar
Murray - well, um, why not?
Anyway, I'm not saying all those are correct but I think they're pretty good guesses.