Ib and The Witch's House are the two best RPGmaker horror games. Ao Oni is fun but repetitive. Misao and Mad Father (the latter is a sequel/spiritual successor to the former) are good ideas with poor execution (and sexual assault). The Crooked Man and its various companion games are pretty spoopy but somewhat lacking in compelling story. I can't think of many more off the top of my head that were any good or particularly memorable. Blank Dream is kind of horror-y I guess.
As far as non-horror games, the LiEat series is really cute, although I'm not sure it's available for free anymore (the collection recently went up on Steam). It has unsettling moments but it's not a horror series. Star-Stealing Prince is an amazing traditional RPG, as is Capella's Promise. Pom Gets Wifi is an entertaining parody that ends up being a really endearing game in its own right. To the Moon is another game made in RPGM that ended up on Steam, it's lovely and you will cry yourself to death.
Re: RPGMaker Games
As far as non-horror games, the LiEat series is really cute, although I'm not sure it's available for free anymore (the collection recently went up on Steam). It has unsettling moments but it's not a horror series. Star-Stealing Prince is an amazing traditional RPG, as is Capella's Promise. Pom Gets Wifi is an entertaining parody that ends up being a really endearing game in its own right. To the Moon is another game made in RPGM that ended up on Steam, it's lovely and you will cry yourself to death.