The only game to come up to my mind that had this villain thing done right was, besides Half-Life 2, GTAIV. GTA Vice City didn't had a single villain from start to finish, it kinda had "commrade turned bad guy" almost at the end of the game, and it had a couple of crazy mobsters, but none of them did anything specific for you to build that negative empathy.
GTAIV on the other hand, had Demtri Rascalov. The only thing he was missing was an evil laugh, but everything this article checklisted, this guy has them all.
Be Onscreen - He's onscreen almost from start to finish. He doesn't get a lot of screen camera time, but also has enough pressence to know his character and to really hate him. He even doesn't kill his own henchmen to demonstrate his villainy!
Do Villainous Things - He made you kill his own best friend (BFF), he burned to ashes your appartment, he tried to kill you many different times, he even tried to kill your cousin many different times and at the right circumstances, ends up killing one of the main characters of the story.
Be a character - Right before you start hating him, you kinda like him, he's like that little voice telling Mikhail (his BFF) to please "stay calm". You even got the time to know he has lots of friends/contacts that not only know him, but they respect him as someone who has done many favors, they even see him as a friend.
Beating the villain has to feel good - You get to kill him, but first you need to get to him in one of the most difficult missions the game has to offer.
Make Your Cut Scenes Count - He doesn't have lots of cutscenes, but simply enough to get to know/hate him.
Get Your Hate On Early - You get to know him pretty early on the game and when he starts doing villainous things, that's when the story really starts to build up.
Remind The Player - Sometimes, you kinda forget why you hate him until he calls you from time to time to remind you how much he wants you dead and sometimes he even sets you a trap of somekind, or kidnaps your cousin, he even sends you a picture of him tied up and bleeding.
Henchmen Are Your Friend - Thank goodnes he doesn't kill his own henchmen, but he does indirectly by sending hundreds to kill you.
Don't Just Take Them Out of the Plastic - He helped your cousin by sending him to the hospital when Mikhail shots him, in some of the conversations with Mikhail, you get to know they are very close friends (BFF), they endured very harsh times to get where they are. He even had a very tough decission by asking you to dispatch his own best friend.
It's no secret GTAIV has the best story a GTA game has to offer and this is one of the reasons why it's a great story.