Great idea for a thread, welcome.
Anyway, off the top of my head here's a list (admittedly my favourite puppeteer is probably going to feature alot, and then my second favourite seems to be in here a fair amount too)
1. Annie Sue Pig - I just HAVE to choose her. Great idea, and a wonderful way to try and make a rather new up and coming puppeteer (as she then was) an integral part of the team on TMS.
2. Female Fish Singer - The fish singer (she's on the Dizzy Gilespie epsiode of TMS) has such a wonderful voice.
3. Lou The Jugband Lady - another great singer
4. Pops The Doorman - He delivered some great lines.
5. Cowboy Jerry - another great singer. Perfectly paired with Lou.
6. Ethel Mermaid - I don't usually like parodies of Merman, but this one really works.
7. Anyone's Nose Singer - OK I just like that voice.
8. Julius Strangepork - a fun character, who delivers some good lines on TMS.
9. Big Mamma - well she was one of those really unpredicatable monsters. A bi of a character.
10. Louisey - just the best foil for Herry Monster's singing talents.
Well that's a quick answer.