To help narrow things down/limit things a bit ill only be considering those among My Favorite Movies which is limited to 151 movies...
Female...1)Liana Telfer (Lena Olin) - The Ninth Gate (1999)
2)Jeanette the Dutch Assassin (Marie-Josée Croze) - Munich (2005)
3)Mathilde (Thekla Reuten) - The American (2010)
it's actually more difficult than I thought it would be to find more legitimate female villains when strictly sticking to movies I consider favorites and that are worth mentioning. The Hateful Eight (2015) / Kill Bill / Face Off (1997) would probably be the best I could come up with outside of the those handful I thought was worth listing above which would pretty much make for five if you count those.
NOTE: there is some others I might have considered but it's somewhat debatable if they are actually villains and I wanted things to be a bit more clear cut in my choices.
NOTE: my 2nd/3rd choices I ended up listing are both assassin types and both the two movies themselves are pretty close as Munich is a 8-8.5/10 and The American is a 9/10 for me. even my #1 choice is a 8-8.5/10 for the movie itself.
Male (in no order)...-Maguire (Jude Law) - Road to Perdition (2002) (surely one of my very top choices for villains)
-Frank (Henry Fonda) - Once Upon a Time in the West (1968)
-Silva (Javier Bardem) - Skyfall (2012)
-Bert Gordon (George C Scott) - The Hustler (1961)
-Mr. Earl Brooks (Kevin Costner) - Mr. Brooks (2007) (NOTE: for a leading role villain... this has to be within my Top 2)
-Boris Balkan (Frank Langella) - The Ninth Gate (1999)
-Alejandro Sosa (Paul Shenar) - Scarface (1983) (hell, he makes the list just for the lines... 'Don't F me Tony, don't you ever try to F me' and 'I told you a long time ago you Fing little monkey not to F me!'
)
-Tony Montana (Al Pacino) - Scarface (1983) (for a leaking role villain this has got to be within my Top 2)
-Bodhi (Patrick Swayze) - Point Break (1991)
-Jacob/Money (Nikolaj Coster-Waldau (the guy from Game of Thrones)) - Shot Caller (2017) (this has to be my #1 villain in the regard he changed from good to bad)
-Calvin Candie (Leo Dicaprio) - Django Unchained (2012)
-Stephen (Sam Jackson) - Django Unchained (2012)
-Ray Ferritto (Robert Davi) - Kill the Irishman (2011)
-Mr. French (Ray Winstone) - The Departed (2006)
-Nicki Santoro (Joe Pesci) - Casino (1995)
-Don Vito Corleono (Marlon Brando) - The Godfather (1972)
-Don Michael Corleone (Al Pacino) - The Godfather trilogy
-Ray Marcus (Aaron Taylor-Johnson) - Nocturnal Animals (2016)
-Killer Joe Cooper (Matthew McConaughey) - Killer Joe (2011-2012)
-Charley Rakes (Guy Pearce) - Lawless (2012)
-Bernie Rose (Albert Brooks) - Drive (2011)
-The Accountant (William Fichtner) - Drive Angry (2011) (this one is a bit more unique on the list as it's more of a cool/fun kind of villain instead of more of the serious types that I typically have listed in this topic)
-Frank Lucas (Denzel Washington) - American Gangster (2007)
-Verona (Jose Pablo Cantillo) - Crank (2006)
-Castor Troy (Nicolas Cage) - Face/Off (1997)
-Howard Payne (Dennis Hopper) - Speed (1994)
-Jules Winnfield (Sam Jackson) - Pulp Fiction (1994) (the end scene at the dinner is hard to beat)
-Franz Sanchez (Robert Davi) - Licence to Kill (1989)
it's much easier to come up with male villains than it is female villains among My Favorite Movies. so instead of listing five male villains ill just list those I felt are worth mentioning, or thereabouts. I might have left a little off the list and some might be able to be removed from the list if I was trying to really narrow things down. but ill leave things as it is for now.