Growing the Beard: As the series went on, the writing and the voice acting got increasingly better. In particular, Purple's voice acting was quite lackluster in Episode 2, but has improved much more since.
Especially HadoukenDude as Green Link. In the original version of Episode 1, his performance suffered from Dull Surprise. Like Purple's VA, he's thankfully gotten better.
Hilarious in Hindsight: In the second part of the Broken Mirror arc, when trying to teleport back to the main entrance of the first dungeon, they briefly stumble into the first Legend of Zelda game, complete with the appropriate graphics, causing Red, Blue, and Purple Link to shout in unison "GOOD GOD, NO!" In the anniversary release of Four Swords, one of the levels for the Realm of Memories that the Links could play in is a level based on the first Zelda, down to the graphics.