DannyGE

This is just a short list:
Macaron-kun from 30-sai no Hoken Taiiku
Lag Seeing from Tegami Bachi
Reg from Made in Abyss
Usamaro from Ao no Exorcist Movie
Kyuuta from Bakemono no Ko
Satoru Fujinuma, Kenya Kobayashi and Hiromi Sugita from Boku dake ga Inai Machi
Tomoki Himi and Lucemonfrom from Digimon Frontier
Chuutarou Kumou from Donten ni Warau
Dororo from Dororo (I know is a loli but I looked her as a him for a long time)
Trunks and Goten from Dragon Ball Z
Naota Nandaba from FLCL
Haruka Nanase, Rin Matsuoka, Nagisa Hazuki and Makoto Tachibana from Free! (as kid´s versions)
Kokkuri-san from Gugure! Kokkuri-san (as kid version)
Remy Odhner from Gunslinger Stratos The Animation
Hasuta from Haiyore! Nyaruko-san
Ayumu Hoshino from Hoshizora e Kakaru Hashi
Shuuichi Nitori from Hourou Musuko
Banri Watanuki and Miketsukami from Inu x Boku SS
Taiki and Enki from Juuni Kokuki
Ernesti Echevarria from Knight's & Magic
Ciel Phantomhive from Kuroshitsuji
Ryouta Satou, Tsubasa Kawai and Koji Imai from Kyou no 5 no 2
Haru from Last Period: Owarinaki Rasen no Monogatari
Ritsuka Aoyagi from Loveless
Aladdin from Magi: The Labyrinth of Magic
Yuu from Merc Storia: Mukiryoku no Shounen to Bin no Naka no Shoujo
Makoto from Minami-ke
Tooru Muhyou from Muhyo to Rouji no Mahouritsu Soudan Jimusho
Haruhiko Ichijou from Musaigen no Phantom World (as kid version)
Hikari Sakishima and Akira Shiodome from Nagi no Asu kara
Yukine and Ebisu (Eeincarnated) from Noragami
Tomoya Mizuhara from Oneechan ga Kita
Ren Mihashi from Ookiku Furikabutte
Mitsukuni Haninozuka from Ouran Koukou Host Club
Mira Munakata from Papa to Kiss in the Dark
Aoyama from Penguin Highway
Maro Kitahara from Piace: Watashi no Italian
Yuuta Iridatsu from Punch Line
Yoshio Kobayashi from Ranpo Kitan: Game of Laplace
Takumi from Strange+
Takeru Aizawa from Shinryaku! Ika Musume
Curo Kazamiya from Shounen Maid Kuuro-kun: Tenshi no Uta
Kazuma Ikezawa from Summer Wars
Ren Kaidou from Super Lovers
Rimuru Tempest from Tensei shitara Slime Datta Ken
Poko from Udon no Kuni no Kiniro Kemari
Shun Aonuma, Satoru Asahina and Mamoru Itou from Shinsekai yori
Yuuma Kuga from World Trigger
Albus from Zero kara Hajimeru Mahou no Sho

And those are only some of my favorite already watched anime´s shotas caracters