>>3I'm surprised you put WW so low. A lot of it was implicit, but the idea of the new taking over from the old was probably the most mature Zelda theming to date.
Ganondorf's inability to let go of the old kingdom even though he was the only one in it, Link having to earn his place as the hero, rather than being born into it; 'I want you to live for the future!' – all great moments. The reworking of old music definitely helped, too.
I'd say Majora's Mask first, because I'm a sucker for mystery, then OoT/WW joint second, as they function best as two sides of the same coin, like Tolkien's Silmarilion and LotR trilogy. After that I'd say LA, TP for Midna, LttP for establishing a lot of the canon, and SS for Demise. I don't remember anything particularly striking about OoA/S, and funnily enough, I haven't played Phantom Hourglass or Spirit Tracks, either.