I wasn't going to respond to this thread at first but then I found the concept rather intruiguing, so here goes...
The Muppet Movie
Favourite: Rainbow Connection
(Side note: Three other songs came close)
Least favourite: Never Before, Never Again (although the accompanying footage is hilarious)
The Great Muppet Caper
Favourite: Hey, A Movie
Least favourite: The Muppet Fight Song
(Side note: Piggy's Fantasy, which was dissed repeatedly earlier in this thread, is one of my favourite Muppet sequences of all time)
The Muppets Take Manhattan
Favourite: Saying Goodbye
Least favourite: I'm Gonna Always Love You
The Muppet Christmas Carol
Favourite: One More Sleep 'Til Christmas
Least favourite: Marley and Marley (I never thought this was a good idea)
Muppet Treasure Island
Favourite: Cabin Fever
Least favourite: Sailing For Adventure
Muppets From Space
Favourite: The Gambler
Least favourite: Celebration
(Yes, I'm being completely serious)
It's a Very Merry Muppet Christmas Movie
Favourite: Everyone Matters
Least favourite: Moulin Scrooge (With the exception of Santa Baby)
A Muppet Christmas: Letters To Santa
Favourite: I Wish I Could Be Santa Claus
Least favourite: The opening number in the post office (whose title escapes me)
The Muppets
Favourite: Life's A Happy Song
Least favourite: We Built This City (I couldn't make myself pick any of the Muppet songs, or even Let's Talk About Me)
I have no comment on The Muppet Wizard of Oz because I haven't seen it in five years and its music really didn't make that much of an impression on me.