As for Zelda, I now personally think Twilight Princess is better than Wind Waker, but not much. Wind Waker has the better story, and it's more "Zelda", and it's more "GameCube" than Twilight Princess is "Wii" but still Twilight Princess is a little better.
The biggest thing they could do to the series, as of now, is add voice acting. But then again, we all know from Super Mario Sunshine that voice acting isn't exactly Nintendo's cup of tea, but who knows? Some series, like Final Fantasy, don't get off to a good start with voice acting but they improve later. Some, like Metroid, are immediately blessed with great (if infrequent) voice acting from the get-go.
Say, isn't it a little odd that Metroid, a series that NEVER has NPCs, except in Prime 3 Corruption, has voice acting, while Zelda doesn't. It should really be the other way around, but then again (I was going to say that I can't imagine Metroid with text speaking, but I forgot that Metroid Fusion has it).
BTW if you want to hear Link speak, you have to play Wind Waker, get to the Tower of the Gods, and call a statue to come moving for you.
Also, if you might have noticed, using a projectile in Wind Waker (or Ocarina of Time or Majora's Mask) is in a first-person perspective, while in Twilight Princess it's in an over-the-shoulder perspective, just like Resident Evil 4 or Gears of War (man, I think we all know how influential Resident Evil 4 is for this current generation, much like Ocarina of Time was in its days and the last generation).
Remembering Gamespy's list, PC titles like Diablo, Wasteland, X-Wing, and Star Control II were there. So...