As far as comic book movies go, I think Loki and Magneto are the 2 best villains of the Marvel universe so far.
Likewise, Nolan's Joker and Bane are the 2 best villains from DC.
All 4 of these actors definitely captured the true essence of these villains.
But I think Heath Ledger gave the very best performance out of all 4. Hands down.
Especially when you look at all his quirky mannerisms, nervous ticks, vocal inflections and maniacal traits that he incorporated into his version of the Joker.
With no superpowers at all, the Joker remains the most dangerous, intimidating & totally unpredictable villain we have seen onscreen in all the Marvel & DC films combined.
Loki is second. Followed by Magneto & Bane tied for third in my book.