For this task, I think I'm going with some of the great classics that helped establish the hero / villain dichotomy ... as well as its recently most successful reincarnation:
1. Sherlock Holmes vs. Dr. Moriarty (and in pastiches, vs. everybody from Jack the Ripper to Count Dracula ... as well as ... really just everything, including boredom, as BT just reminded us)
2. The Four Musketeers vs. Cardinal Richelieu and Milady
3. Edmond Dantès aka The Count of Monte Cristo vs. the conspirators Mondego, Villefort and Danglars
4. The Hobbits, Gandalf and The Fellowship of the Ring vs. The One Ring, Sauron and Saruman
5. Harry Potter and his friends vs. Lord Voldemort and the Deatheaters