1.) The Fire Rod (A Link to the Past, Link's Awakening)

Ah, the Fire Rod.  One of the best items in ALttP and LA.  And those are the only games we've seen it in, and it's a shame we haven't seen it since.  The Fire Rod (or the Magic Rod in LA) could burn through anything.  And it was even better in LA for two reasons.  A) You didn't have to worry about running out of magic to use it.  B) You could kill cuccos and those dogs in Mabe Village with it.  No, seriously, you could.  If you still have LA, or downloaded it for the 3DS, go try it out.  I'll wait.

2.) Compass (Link's Awakening)

Okay, yes, this item has been in nearly every Zelda game.  However, I'm talking specifically about the compass in LA.  Do you remember it?  It had that fancy new feature that let you know if a key was hidden in the room when you entered it.  It was a pretty handy feature when you entered an empty or enemy-filled room, but couldn't see anything that would help you.  You heard the tone, and knew you shouldn't skip this room.  I don't know why they took this out.  If you know, let me know.

3.) Bees (A Link to the Past)

Other Zelda games had bees, but they were only given enemy status, and one that you could avoid if you left them alone.  But in ALttP, you could use your Bug Catching Net for its intended purpose (unless you think faeries are insects) and catch a bee.  Then you could take the bee out later, and it would attack enemies for you.  The only problem was that it flew off afterwards, unless you re-caught it.  And you'd probably have to be quick about it, too.  I don't know; I never bothered with the bees.  That's because the Golden Bee was better.  It flew around you, and as soon as an enemy was in sight, it went into killing mode.  And when the enemy was stung to death, it flew back to you.  You had to re-catch it before moving on to the next screen, but at least you didn't have to chase after it.

4.) Stronger Armor (A Link to the Past)

Barring shields, several Zelda games had ways to decrease the damage Link took.  In ALttP, this was accomplished by getting the Blue Mail, and later the Red Mail.  This is an aspect I miss.  Sure, Link's Awakening DX had the Color Dungeon, but the blue tunic was optional (I always took the red tunic on the principle that the sooner you kill the boss, the fewer chances it had to hurt you).  Twilight Princess had the Magic Armor, but that required rupees for it to work, and when you ran out you were screwed.  I think ALttP had it best.

5.) Silver Arrows (The Legend of Zelda, A Link to the Past)

The arrows that were necessary to slay Ganon once and for all, or at least until one of his minions resurrected him.  I've never actually checked this, but I think the Silver Arrows were stronger that regular arrows, and I see no reason to doubt this (at least until someone corrects me).  Ocarina of Time, Majora's Mask, and The Wind Waker had stronger arrows in the form of the Fire, Ice, and Light Arrows, but they're just not the same as old school Silver Arrows.  Don't get me wrong, those arrows were cool, but they could be even more awesome when combined with the Silver Arrows.  Just try to tell me you don't want to see that.

6.) The Medallions (A Link to the Past)

You know the medallions I'm talking about.  Bombos.  Ether.  Quake.  They unleashed a powerful, screen-wide spell that just decimated your enemies, and the Ether and Quake medallions were actually required to beat the game (you know, to get into Misery Mire and Turtle's Rock, respectively).  Okay, so you couldn't overuse them, or you'd run out of magic, but that didn't stop them from being cool.  Any Zelda game with a magic meter should bust out these spells again, especially the 3D Zelda games.  Just imagine what that would look like.  Are you imagining awesomeness?  I am.