"Jill" for the female player characters, until their names were eventually revealed to be Claire [the blonde] and Pony [the brunette].
Many people refer to any of the male protagonists without an ingame default name as "Jack" despite the fact that the Wonderful Life "Jack" is "Mark", the Magical Melody one is "Tito", the Save The Homeland one is Tony, and most others up until IOH were called "Pete".
The Grand Bazaar protagonists have no official names yet, but the fans call then "Hansel" and "Gretel".
Marth Debuted in Smash Bros.: To newer fans, this occurs quite often when characters from older games appear in newer ones. Sara for example appeared for the first time in around ten years in a Wiiware game, and her source games are obscure Game Boy games; thus obviously some people thought she was a new character. Characters from the first game in the series have been mistaken for copycats of the Harvest Moon 64 characters, who are actually made as descendants of the originals.
Urban Legend of Zelda: The perma-locked sheds in A Wonderful Life, the many non-existent ways to open them, and the many little animals running around the valley wearing neckacheifs, and the many ways to 'recruit' them onto your farm. Becomes Ascended Fanon in Sunshine Islands: once you raise Animal Island, you can befriend the animals there and have them do certain chores for you - like gathering lumber and grasses.
In A Wonderful Life there was supposed to be circus. The characters were scrapped, and eventually used for DS. For the enhanced edition, instead of a daughter that resembles the father your daughter was supposed to have multiple looks (similar to your son) but was scrapped due to technical limitations and time.
In Tree of Tranquility, there's a slower, more ethereal-sounding, alternate mix of the Spring music that plays in the Sundae Inn at night throughout the year. It's really quite lovely. So, what could have been, you ask? The BGM tester in the Configurations menu reveals three other similar mixes, corresponding to the other three seasonal themes, that do not show up in the actual gameplay. It's quite possible the evening theme at the Sundae Inn was supposed to originally change according to the season, but since it stays with the slower Spring music throughout the year, it's hard to tell.
Animal Parade, incidentally, also features slower, remixed versions of the seasonal themes that pay at nightfall. These actually play in-game, when you're out on the field, running around, and they change according to the season. Fugue Forest's swamp section and Toucan Island even have their own slow nighttime music. It's also possible that, in Tree of Tranquility, the slower variations of the seasonal themes were supposed to kick in outside, during nightfall, and for whatever reason, it was scrapped in favor of the traditionally silent evenings the series usually has and the nighttime spring music just got shoved into the inn.