I don't know if I have a favorite but there are some for me that still stand out and I use:
a) Enemies I - one of the first books I ever got, nuff said
b) Enemies II - I think I like this one even more than I above.
c) Classic Enemies - this is a good addition but quite frankly, I felt the new versions of Eurostar were powergaming versions and never use them. However, the art is a wonderful revision, in particular Panda, Herculon and Leech.
d) Enemies: International - I kinda like this and at the same time don't. The art is mediocre for the most part. Some of the villains felt like the author was stretching to create villains to fill out the book so for the campaign. Only a few are used now (the rest cured, locked away, etc)
e) Conquerors, Killers and Crooks - quite good. However, I felt the villains almost always having 2 pages each was unnecessarily detailed. There's alot of information on each villains as well as 3 plot hooks for each. However, with 2 pages for each, I've occasionally ended up putting them on spreadsheets streamlining them to 1 page; flipping through pages during an episode slows things down & makes me as GM look like I don't have the episode ready.