I'm seeing a fair amount of consensus on some entries that didn't make it, such as Babel Fish. They must have been close... I'm also mildly disappointed at the lack of Zelda and Mario enemies. Great list, though, and great writeups from Darwin.
1. Mushi
2. Pikmin
3. Catbusses
4. Sky Bison (Avatar: The Last Airbender)
5. Pequeninos / "Piggies"
6. Wookies
7. Ents
8. Susuwatari (the soot sprites from various Studio Ghibli films)
9. Grue (Zork)
10. Oni
11. The simple Hyperchicken
12. Babelfish
13. Irken
14. Time Lords
15. Lumpy Space People ("Oh, my, Glob. I cahn't believe you fohrgot LSP and like all her best friends! I'm never speaking to you again, like, evar.")
16. Totoro
17. Yoshi
18. The Cuties (The fierce little guys that just fall apart in Adventure Time)
19. Kodama

There really needs to be an endless chorus of soft Kodama clattering you can pull up like
Rainy Mood. Someone get on that.
20. Lizalfos ("Aah-AHK!")
21. Nibblonians
22. Moblins (The Legend of Zelda: Windwaker)
23. Shadows (Babylon 5)
24. Piranha Plants (Super Mario)
25. Shinigami
On my list of about 70, I did have Candy People, as well as the Rump People and the Pagelings. I'm pretty surprised that (my) Little Ponies made it on, since they were bumped down to 34 on my list. I also had Trandoshan and Djinn down there; kudos to those who included them.