Sephiroth (aka Lance Bass' greatest role) is one hell of a villain for a couple reasons - mainly for famously and dramatically killing off party member and supposed love interest Aeris midway through the game, stabbing her through the back with his wayyyyy too long sword. But beyond that, he burns down villages and goes on corporation murder-sprees and tries to wreck the entire planet, so maybe impaling one praying flower girl doesn't really compare. Regardless, he's yet another Final Fantasy villain who decides to become a god and tear up the world - although what probably gives Sephiroth the edge is his sweet theme music: One Winged Angel.
Someone with music that badass gets a pass on trying to bring about the apocalypse.
If nothing else, Bowser is persistent. He's tried kidnapping all manners of princesses, Mario, and pretty much whatever else he can find lying around in his attempts to conquer the Mushroom Kingdom and beyond. And luckily he's a good sport about it all - willing to hang out with Mario 'n pals whenever they go golfing or go-karting or whatever. Business is business with Bowser. He doesn't take it personally when Mario dunks him in lava - or when Mario does it again to his skeleton. Hell, Mario's murdered his kids and countless troops of his, and he still keeps a positive attitude and doesn't hold a grudge. Classy guy, that Bowser.
Ganon's got it rough - all he needs to do is take a quick glance at the history books and he can tell instantly what's about to happen. He's there, he'll try pulling a fast move to take over Hyrule (usually involving kidnapping a certain princess), then some punk kid named Link will show up and ruin everything. But that never gave Ganon pause - as the sole male Gerudo and the frequent holder of the Triforce of Power, Ganon gives each battle his all. He put up with several pan-dimensional imprisonments, he fought off time-traveling Kokiri kids, and he was great at energy ball tennis. Not bad for a beeping pig-man.
First off, YES - The Joker is primarily known as a "comic book villain" - but the great thing about characters from ANY form of media is that they can be reinterpreted on other kinds of media and those portrayals remain distinct and interesting. Is Heath Ledger's Joker not a good movie villain?
Anyways, not too sure why we feel the need to defend this choice, since it was you - the voters - who put him in number two.
The Joker is what tied together the first two Arkham games - and Mark Hamill's brilliant vocal performance (more specifically, his amazing Joker laugh). He was still the psychotic, maniacal clown that everyone's come to know and love, but the fact that a fully-realized homicidal Joker was appearing in bigtime videogames was a huge deal. That was really the sign that these were licensed games that weren't unplayable garbage: the developers cared about getting the Joker right. They cared about everything else too, but getting the Joker right is pretty essential for a Batman game.
Pretty impressive there were two mass murdering clowns on this list. Could've gone for three if they'd ever made an "IT" videogame.
GLaDOS (or "Genetic Lifeform and Disk Operating System," or "That Orphan-Hating Computer Lady") is the primary antagonist of Portal 1 and some of Portal 2. And she's incredible - she's mean, cruel, hilarious, dry, and threatening. She's everything you could possibly want from a villain - she'll force you to destroy the one thing you have any emotional attachment to, just for kicks. She'll destroy all evidence of her old consciousness so that none of her basic humanity seeps in. She'll get vengeful as hell against the damned orphan who tried to mess with her precious tests.
What makes GLaDOS not only a great villain but the BEST villain is that she gets it. All of the other villains here are too egomaniacal to consider not succeeding a possibility. They're willing to fight to the death, because they're convinced they can't lose. GLaDOS comes to a realization though - it's just not worth it. She's not gonna be able to beat Chell, so screw it. It's not worth the effort and the heartache to be locked in battle with a worthy opponent. That's the kind of stuff that leads you to getting trapped as a potato.
But maybe best of all - she'll play you out with a song.