Skyward Sword, The Wind Waker, and Phantom Hourglass are the three funniest Zelda games, in my opinion. I regard them as the funniest because of their fantastic comic relief characters, such as Groose and Ghirahim in SS, Tetra and the pirates in TWW, and Linebeck in PH. These games also had very funny moments involving Link: for example, Link's facial expressions before being cannonballed into the Forsaken Fortress in TWW, and some of Link's reactions to Groose's statements towards the end of SS.
Overall, I'd have to give the crown to Skyward Sword as the funniest Zelda game. Groose's demeanor and character development were perfect; they were both humorous and story-driven, which made them even better. Groose's initial reaction to the land below and him saying it was all the Legend of Groose at the end of the game were priceless. Also, Ghirahim was a very fabulous interesting character, to say the least. Him licking his chops just never gets old, does it? And to go along with those two very funny characters, the supporting cast supplied some pretty funny moments as well, especially during sidequests: including Fledge, Batreaux, and a few others.