In their newest issue (don't ask why I'm still getting the magazine in the first place), Nintendo Power made decided to rank every Zelda game that has been released, as well as picking their favourite item, dungeon, boss, etc. of all time. Though I strongly disagree with most of the choices, here's the list:
13: Adventure of Link
12: Four Swords Adventures
11: Majora's Mask
10/9: Ages/Seasons (NP gives the advantage to Seasons, citing Rod of Seasons > Harp of Ages)
8: Minish Cap
7: Phantom Hourglass
6: Wind Waker
5: Link's Awakening (the original and DX were grouped together)
4: Twilight Princess
3: The Legend of Zelda (the original)
2: Link to the Past
1: Ocarina of Time
Best...
Weapon: Bow
Hook: Light/Dark World (LttP)
Item: Double Clawshots (TP)
*Princess* Zelda: Wind Waker
Boss: Argorok (TP)
Overworld: Minish Cap
Story Moment: Beneath the Waves (WW)
Tune: Overworld Theme (TLoZ)
Secret: Second Quest (TLoZ)
Dungeon: Goron Mines (TP)
Enemy: Octorok
Supporting Character: Midna (TP)
Ganon: Ocarina of Time
Feel free to rant all you want.
EDIT: I'm gonna make my own lists, I suppose.
Games:
13: AoL
12: FSA
11: PH
10: WW
9: TP
8: OoS
7: MC
6: OoA
5: TLoZ
4: LA
3: LttP
2: MM
1: OoT
Seeing TP lose to all four games to be released on the GB/GBA makes me happy.
Best...
Weapon: Sword
Hook: Light/Dark World (LttP) (Wow, I actually agree with NP on something)
Item: Ocarina
Princess Zelda: OoT
Boss: Smog (OoA)
Overworld: Oracle of Ages
Story Moment: Zelda/Sheik revealing
Tune: Ballad of the wind fish (LA)
Secret: None
Dungeon: Shadow Temple (OoT)
Enemy: Octorok
Supporting Character: Ezlo (MC)
Ganon: Ocarina of Time