Guys. We're getting waaay off topic. For starters, we're in the "Zelda Theory" section, which means we're supposed to be discussing/debating a theory, not just picking which we like best and why. If you'd read the first post before posting, you've noticed this...
Okay, onto an answer of sorts...
When I was playing WW, PH, and ST, I noticed some similarities between Links from oter games and the Link who has come to be known as Toon Link. Also to offer an explanation to the differing time lines, are the different Links supposed to be reincarnations of the original? I think this would explain a lot.
I think the confusion first arises from Smash Bros Brawl, where it lists "Link" and "Toon Link" as being seperate characters. The truth is, they aren't. They're both just different incarnations of "Link". The reason they're listed under seperate names is to avoid confusion on the character select screen, so you didn't have a LINK and a LINK.
Obviously, most of the Links are different guys, but you're right, they do all share common traits. This has lead some to theorize that they are in fact the reincarnation of the same guy (some would point out that there are a few quotes here and there in the games that seem to suggest this), but just as likely they simply could all be incarnations (different to a reincarnation) of "the Hero" that appears in Hyrule in times of need... and as Locke said, they just look alike for familiarity... or possibly they're all related and each are a different generation in a bloodline (again, some would say there's some evidence for this too...)
Honestly though, no one really knows... so it's up to you to make up your mind XD
Also, just to clear this up if it needs to be... the way you mention WW, PH and ST Link makes it sound like he's the same guy XDD Correct, they all count as being a Toon Link, but only WW/PH Link is
the Toon Link mentioned in Brawl. ST Link is a seperate Link entirely to WW/PH Link :3