Hrmm.. Let me see. One of my favourite pointless little things in the Zelda games are jumping off high things. Such as in TP in Kakariko Village in the very tall outpost. Or Outset Island in Wind Waker.
I couldn't agree with this more. Like you said, Kazumi, in the Wind Waker, you could jump off the big cliff on Outset Island in the Wind Waker. I also liked bringing little pigs up there and just throwing them off. You could also bring the Big Black one (named after Link) up, put on the iron boots, and then fall down, and the pig would go through the rock. Cool little glitch right there.
In OoT, it was fun to put on the masks and scare people in Hyrule Castle Town (I think that's what it's called), I loved their reactions. And while no one ever reacted strangely, it was fun to Z-target random people in Clock Town in MM and then do the Kamaro Mask dance. And that's just one of many pointless things I like to do with masks in that game.
And in PH, all the priceless Linebeck cutscenes. They all made me laugh. Sometimes quite a bit. I especially liked the one at the end of the Ghost Ship, where he knocks down Tetra's stone-covered body in the Background, then struggles to get it back upright. I also loved how right when you first meet him, and you've saved him, he shakes Link a bunch, and once he gives him the key, he's all shaky, and wobbling around everywhere. Just classic.
In TP, I would go around in Hyrule Field, and kill enemies with the Jump Strike. The Jump Strike is the most amazing move ever, and Link's yell when he does it is awesome. I was way to obsessed with that thing my first playthrough of TP. I pretty much killed every enemy I could with it.