I can think of a few...
hookshot (I don't know how you'd script it either, though) - Depending on what you hit, you'll be pulled towards it, it will be pulled towards you, or nothing will happen.
throwing items (you mentioned this already) - You can throw stuff, like pots, bombs...nuf said
"connected attacks" - I dunno if this is the combo system you mentioned, but one feature is how after you swing once, the second consecutive swing will use a different sprite sheet. However, if you pause for more than a second or so between attacks, the next attack will use the first sprite sheet.
enemy "weak points" - I dunno if you can do this already, but you probobly know what I mean. Making a boss only hurtable in one spot, like the crsystal on the four head (at least one or two bosses per zelda game have that weakness

)
bottles - you know, catching stuff in bottles (like fairies). I can't think of a way to do this with events
That's all that comes to mind, except a few features that very few people would ever end up using (like rolling into a ball when you're in goron form). Hope that was useful.