Antagonists are just as important as the protagonist, if not more important, because they usually provide the reason for seeing a story through to the end.
As for who my favorite is, I've got to say Andrew Ryan from Bioshock. He is so seemingly crazy, always killing off anyone trying to help Jack in his quest for god-knows-what. But he also is educated, and has many great things to say that give the player food for thought, "We all make choices, but in the end, our choices make us!" and "A slave obeys, a man chooses!" have both been used by me in essays for school. Andrew Ryan is the perfect antagonist, although the actual villain of Bioshock was yet to be seen...
As for who my favorite is, I've got to say Andrew Ryan from Bioshock. He is so seemingly crazy, always killing off anyone trying to help Jack in his quest for god-knows-what. But he also is educated, and has many great things to say that give the player food for thought, "We all make choices, but in the end, our choices make us!" and "A slave obeys, a man chooses!" have both been used by me in essays for school. Andrew Ryan is the perfect antagonist, although the actual villain of Bioshock was yet to be seen...