Meruem is my favorite ANTagonist, although terrible puns aside I don't really like considering him one, he's kinda closer to the protagonist role in that arc honestly, but Meruem is probably the best developed character I've seen in anime so giving him a shout.
There are some great ones already mentioned (I'm especially partial to Crocodile & Hisoka) but ignoring all those Johan from Monster, Friend from 20th Century Boys, Legato Bluesummers from Trigun, Makoto Shishio from Rurouni Kenshin, Shinobu Sensui from Yu Yu Hakusho, Yoshikage Kira from JoJo's Bizarre Adventure: Diamond is UnBreakable, Misogi Kumagawa from Medaka Box, & Squeler from Shinsekai yori are all among my favorites as well.
Not sure how I'd rank them, Makoto Shishio is probably my favorite because of his fire theme, his cool design, Steven Blum, the way his fight's built up, the fight itself, and just how much he serves as a contrast to Kenshin Himura. The best antagonists should serve in conflict to the ideology of the protagonist, and the parallels of Manslayers between the two at the beginning of the arc is really neat. But I could make arguments for most of them, Kira is the most idiosyncratic and tangibly real of the bunch, Squeler is the most thematically rich and morally complex, Legato has the most iconic moments, Sensui has the strongest parallels with Yusuke and a unique personality set, & Kumagawa is the most amusing.