Clock Town, Romani's Ranch., and Zora Hall.
Clock Town was my first encounter of a video-game town that really had life to it. This wasn't just a place filled with NPC's; things were happening. They were happening now and they were effecting areas around them. There was also the peaceful atmosphere of the first day. I love suburb concepts, even though Clock Town is a town, those blue skies, a playground for kids, a nice little pond to visit, I felt at peace there. Not to mention, this was my first Zelda game, thus all the hidden puzzles and clues in that town blew my mind. Even if this hadn't, the amount of secrets and exploration incorporated in MM has outdone most, if not all, starting towns before and since.
Romani's Ranch had a different, yet still memorable impact. It wasn't the peacefulness of the area, but rather the sudden unexpected events of it. Aliens? Bandits? In OoT, you were required to rescue a horse on the ranch, which is what you'd expect to do. Romani's Ranch is home to some of the most outlandish side quests (not surprising since its in Majora's Mask) and there's so much happening on all three days that it just left a giant footprint in my memory.
Zora Hall was a load off of the chaos that had been going on in MM. I had gone through a town filled with a evil looking trollface moon, a poison swamp with a palace filled with racists plants, a blizzard of a mountain with a crybaby goron, a ranch with aliens and thieves, and a murky ocean with thievery pirates and GIANT EELS THAT WANTED TO KILL ME! Then I entered Zora Hall... my first time ever hearing that music, seeing the peaceful race that is the zoras... I felt so at ease. These were just happy people (well... fish) trying to spread happiness. There wasn't malice in the atmosphere, just peace... even with the troubles they were having. I later came to realize that other Zora territories, OoT and TP, were like this as well, but MM was my first experience with them. If it weren't for Clock Town's suburban like atmosphere, Zora Hall would be my location of choice in Termina to set up my home.