Demons Roots is probably the best RPG Maker game I’ve played that was actually playable as an RPG. (So, not counting things like To The Moon which other people have already mentioned.)

I wasn’t a fan of most of the sexual content in Demons Roots, but taking the whole thing as basically a giant love letter to fucked up doujinshi stories – i.e. to unpolished indie writing with wild genre bending plot twists in addition to the hentai stuff – I can accept it for what it is. The game has that RPGMaker wabi-sabi; it’s not especially well-crafted software… but the combat was OK (unlike a lot of indie RPGs), the music was good – a mix of original and mostly well chosen asset packs (I still listen to some of it occasionally!), and, without getting into spoilers, it did a couple of very memorable things…