Narrowing it down to three is too hard but some of my favourites are:
Paradise Kiss (haven’t read it in Japanese yet)
Life
Flowers of Evil
Watamote
X (what I’ve read of it so far. The art in it is gorgeous - wings! Feathers! Flowers! Gore…?)
GTO
Ushijima-kun
Yotsubato
GTO and Ushijima-kun are quite difficult to read in Japanese. It probably helped me to have read these in my mother tongue before rereading in Japanese several years later.
yeah, makes sense 
My top three would be Dr Stone, Promised Neverland, and Crescent Moon. Crescent Moon is older and only lasted 6 volumes, so it may be hard to find now though. Fruits Basket is also good and was the first manga I ever read.
I do racing manga because that is my interest, so Initial D (duh) and MF Ghost. I also have some Zero Angel, but it’s beyond my level so super hard to read so far.
I am thinking of ordering some of Shigeno’s other stories (sports) as I adore his writing style.