This is actually difficult for me, since I play a number of good games.
I'll give you guys a good top three, 'kay?
{1} WHEATLEY - PORTAL 2
From the beginning of the game, you get to know Wheatley as a talkative-but-helpful-and-funny companion who just wants to get out before things...you know...explode. And, he's not actually BAD. It's just that the plan that put him into charge rapidly-corrupted him from the inside, and...Glados didn't help by revealing his true nature. To me, Wheatley isn't even properly evil. It's this place. It's Aperture Science that's doing it. So, when you're fighting him, remember that this was your friend, the guy that tried to get you OUT. He talks up a storm while fighting, AND his Four Part Plan IS rather good for a guy who's unable to figure out how to keep the labs from exploding. It's a fun battle.
{2} CUBIA - .HACK GAMES
This goes back a while, because of how long ago the .hack phenomenon has been going on. When I played the first game and beat Skeith, alluded to be the first phase of something greater, I didn't know what to expect. The last thing I DID expect was for The World to go crazy, and then at the end of the game to be blasted by a giant hovering monster. When I first saw Cubia, I was shocked. What WAS that thing? Cubia is your daunting shadow throughout the series. Literally, he's some sort of Guardian of The World seeing you as the major threat because all the Phases and Morganna Mode Gone have the right credentials...and you're a kid that Data Drains and has a massive infection. He shows up to prevent you from confronting Aura or ANY key data location out of the belief that it's harmful to the system. In the final confrontation in Quarantine, Kite realizes that this creature will NEVER stop hunting them down unless the Twilight Bracelet is destroyed, leading us into the problem of the final battle without it. Cubia also returns in later games, albeit changed because of the happenings OF those games, and then finally he's compiled into a character 9in .hack//LINK with exceptional ability! Kid's scary, yo, but awesome.
And finally...
{3} KAIN VERSUS RAZIEL - LEGACY OF KAIN: DEFIANCE
Legacy of Kain games are weird and hard to follow at times, and both Blood Omen 2 and Soul Reaver 2 can be frustrating. However, Defiance was hella-good, and so was this culmination in all the backstory and rivalry between these two beings, Kain and Raziel. At the time, Raziel wishes to find the Heart of Darkness and restore Janos Audron, his mind and attitude tweeked by the psychokinetic burst he received from defeating Terel the vampire, possessed by the Hylden who are in fact the source of the Council of Nosgoth's madness. He's realized where the Heart is, but Kain doesn't know, and his impatience and hatred for Kain's scheming leads the two of them to fight it out. This boss fight is a double-act, though, which is why it's brilliant. You start as Kain, trying to bring Raziel to his senses because, for some reason, it's a bad idea to bring Janos Audron back to life. (You find out why later, of course.) And then, once that's done, you switch over to Raziel to defeat Kain at long last, ending in this ending...
Kain beaten with an ironic echo of his own family motto, surprised to find that he was the one to receive the Heart of Darkness.