My guess is if Alyx doesn't win, she'll probably be in the top 10 somewhere. As she should be.

I'm very happy to see Minsc on the list, too. No RPG party is complete without Minsc.
...I do wonder what on God's green earth possessed them to stick Sheva Alomar on that list, though. On any difficulty higher than easy she's, quite frankly, the worst AI companion I've ever run into. Not only do you have to babysit her constantly despite her being armed, but I swear she's been programmed to do the exact opposite of anything helpful. There was one incident in a boss fight in which I put down proximity mines...only to have her come running after me,
picking them all up and giving them back to me.WHY YOU DO THIS, CAPCOM. WHY.
I also had an issue with her picking up ammo before I could and promptly loading it into the guns she never bloody used, owing to her having some sort of sentimental attachment to her pistol. And since for some reason the game wouldn't just let me take/swap guns with her outside the inventory screens at the end of each chapter, I wound up having to restart a level because I was completely out of ammunition and there was a chainsaw man running for my face.
Yup. I had to restart an entire chapter (I was right near the end, too) because my AI ally stole all my ammo and made the game impossible to continue. If that ain't terrible design and programming, I don't know what is.
But they did forget Max from the Sam & Max series of games. Also, I don't see Maureen "Mo" Corley from Full Throttle.
Mo is too awesome for a mere "sidekick" list. True fact.
(Actually, it's more likely that she doesn't fit the traditional definition of sidekick and probably better belongs on a "greatest game characters" list or similar. She's a main character and doesn't accompany Ben as an AI/party companion. ...Also, I give you mad props for thinking of her, sir.

)
The list does fail without Max, definitely. And Glottis. Seriously, Gamespot? How could you forget the http://youtu.be/VxKLz1VKNbs Hmph.