My top five items are the bow and arrow, beetle, whip, bombs, and sand wand.
The bow and arrow may be the most common item in series history, however, Nintendo always finds creative uses for it throughout. I especially beamed at Nintndo's exceptional genius to include the item in Ocarina of Tme's Forest Temple. Shooting Poes and Phantom Ganon emerging from portraits was fantastic. Very creative use of the item in its transition to the 3D plane.
The beetle is one of the greatest items in series history. There is no question about it. The item is used throughout the entire course of the game in nearly every dungeon. By the time I got to the Ancient Cistern, I was amazed to still be using an item I received in the first dungeon. The upgrades were also substantial and I loved grabbing bombs with the beetle's pincers, destroying impediments and subsequently collecting my hard earned rupees.
The whip is a stupendous item. Not only can it be used to swing across large games but also as an offensive weapon. It's designs in Spirit Tracks was fr superior to that in Skyward Sword. In SS, the whip was the last used item which was a huge letdown while in Spirit Tracks it was used in three entire dungeons as well as a minigame with a heart piece on the line.
The bomb is an item which has shown substantial evolution throughout franchise history. In 2D games, you simply placed a bomb and watched it explode. Throwing a bomb in the 3D plane was revolutionary for its time and also highly entertaining. The item took on a new role completely with the introduction of rolling in Skyward Sword. Given all the destructible nooks and crannies the franchise is renowned for, I have a feeling we'll see more creative uses for the item in the future.
The last item I chose to include was one not listed on the poll and that is the Sand Wand from Spirit Tracks. Personally, it was a very unique item and one of the only ones in franchise history without clear offensive purposes. The sand wand fit right in with the more puzzle centered Sand Temple. Not only could it help Link reach higher places but also functioned to stop Ergtorok's dead in their place, allowing Link to ready his sword for the kill. also, stopping the incoming boulders during the Skledritch boss batle was pure genius on Nintendo's part.