For me, all things considered, A Link to the Past is the best Zelda title. I think of subsequent Zelda games and A Link to the Past had the greatest impact on the series. For a game released in 1991, it was just way ahead of its time. The gameplay, the story, the graphics, the music... just everything was amazing.
Sure, A Link to the Past isn't perfect, but I feel that Nintendo made the absolute best possible game they could 15+ years ago. I can't say that about games today. Every game has flaws. I just think that in 2006, some things shouldn't be problems. In Twilight Princess, bosses shouldn't be total pushovers, the overworld shouldn't be empty and so on. Many sequels today, not just Zelda, have some of the same problems of their predecessors.