I'm not sure if I would place PH in second. It was a great game with LOTS of great stuff but it lacked volume and was too easy most of the time. I wish they had added more to every dungeon (I shouldn't be able to beat a dungeon in 10 minutes).
I wish they had made the temple of the ocean king bigger or made more cursed temples.
OMG. I know what would make the best zelda game ever for me. Imagine if they remade for the DS with new items different dungeons and Cursed dungeons (I think the dungeons that would make really cool cursed dungeons are: windfish egg (it would have to be much bigger though), The castle with the golden leaves, and the dream house (this would have to be turned into a dungeon). That game would probably make my year.
oh and all the parallels I can think of between LA and PH
There is an accident at sea, link washes up on the shore, The windfish and ocean king are whales, at the end of the game something wakes up from a dream and the area disappears, the windfish/ocean king has a nightmarish creature in his temple/egg. There is probably more. Post anything else you can think of
my order would be:
1. LA - Best story ever, ending was so perfectly filled with mixed emotions.
2. TP/PH
3. OOT/MC/FS
4. WW
5. MM
6+ everything else (I really didn't enjoy ALTTP very much)