Having started playing those over 10 years ago, im sure I wont do those I played all the justice they deserve going by memory. Oh and Rune Pharmacy was really nice, gotta agree there, even better that we nowadays get at least popular games translated, adds so much to it. But lets see about those I still remember without looking through them all.
Japanese ones: Definitely Sangeki of gear, I like normal RPG's and the battle system in this one was very fun, shows one of the few things you can do with RPGmaker, also everything else is pretty nice too, although on an even older engine of RPGmaker its still enjoyable to me. Plus point, its one of the popular ones that got a decent translation. Thankful for the community there.
Another Japanese one, Treasure Hunter Mai is newer and has more variety in scenes, also fully translated.
And add another popular fan translated one to the mix, Virgin Island, definitely worth it if you like being able to go different routes. Not without reason one of the always recommended games.
Probably more suited to the smaller breast preference would be Lucia Script, Priness of a Age-old Kingdom. Has a machine translation, but if I remember correctly it wasnt so bad, and the game has a nice variety. Especially the shame part played a big role, you had one "scene" in which you could run in and lose again and again, with outcome that changed about 7 times, and even the characters that came to help got involved, very suprising and nice.
Now lets add a collaboration one, as in, the game was made and translated at the same time by a Japanese person and an english translator, and got so far as to be released (although censored) on steam. Meltys Quest is the game im talking about, another top recommended game by most people.
And add another collaboration game, this one was translated by someone that got the agreement of the maker (which isnt very common with japanese game maker). Game is called Fallen - Makina and the City of Ruins. Again, a game that went to the all time top games very quickly not without reason.
Alright thats some of the most popular japanese games, and there are way more that might not be translated, or are for different tastes, or that I dont have in mind right now.
Lets add some western ones, which are the ones that are nearly always named when someone asks for them.
Those would definitely be Noxian Nights, Zombies Life, Legend of Queen Opala series. There are more, but you asked for the all-time favorite, and I named way too many already, not saying others are necessarily bad.
I also mostly go for finished ones, it turned out to be just too much work to play every small update of the way too many games I follow in the western market. But those mentioned by
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for example are all on the watchlist. And I played Zoe's Temptation, my opinion would be that its not necessarily a game that NEEDS to be in RPGmaker, and gets a bit.. convoluted later on, but still enjoyed it. Not a top pick for me personally though.
Holy crap I wrote too much, gonna stop.