As of today (9/5/2015) Here's number of fanfic, catelogued by species on Kurobinega's short stories page.
I think it reflect how popular mamono are among Japanese fandom. Then again, there're "multiple" (and another unknown category) and it's the most popular category. So don't be sad if your waifu seem to be unpopular, she may star in hundreds of harem stories.
That being said, some mamono seem to be surprisely popular...
The number is parentheses is total fic for the mamono, follow by brackets indicate how many new stories since last time (8/25/2015)
- Multiple (976) [+7]
- ヒ・ミ・ツ (98) (guess they're sort of stories without fixed couple?)
(The rest is sorted by number of fic)
- Succubus (137)
- Dragon (111)
- Inari (88)
- Vampire (88) [-1]
- Baphomet (86)
- Lilim (85)
- Lizardman (68) [+2]
- Youko (65)
- Alp (64)
- Shirohebi (57)
- Dullahan (54)
- Gazer (53)
- Werewolf (50)
- Siren (50)
- Medusa (47)
- Anubis (47)
- Gyoubu Danuki (47)
- Mantis (45)
- Witch (44)
- Nekomata (44)
- Doppelganger (42) [+1]
- Cyclops (41)
- Holstaur (39) [+1]
- Dark Priest (38)
- Oomukade (38) [+1]
- Angel (37)
- Kikimora (37)
- Ghost (36)
- Lamia (35)
- Sahuagin (34)
- Elf (33)
- Alice (33)
- Ushi-Oni (33)
- Wight (33) [+1]
- Mad Hatter (33)
- Chochin-Obake (32)
- Kunoichi (32)
- Dhampir (31)
- Wyvern (31)
- Lich (31)
- Nightmare (30)
- Living Doll (30)
- Amazoness (29)
- Orc (29)
- Yuki-Onna (28)
- Nureonago (28)
- Jinko (28) [+1]
- Weresheep (27)
- Devil (27)
- Ogre (25)
- Harpy (24)
- Echidna (24)
- Sea Bishop (24)
- Ghoul (24) [-1]
- Selkie (24)
- Hellhound (24)
- Zombie (23)
- Crow Tengu (23)
- Ryu (23) [+1]
- Alraune (22)
- Red Oni (22)
- Mimic (22)
- Dark Elf (22)
- Werecat (22)
- Minotaur (22)
- Unicorn (22)
- Thunderbird (22)
- Manticore (22) [+1]
- Tentacle (22)
- Pixie (21)
- Nereid (20)
- Yeti (20)
- Glacies (20)
- Valkyrie (20) [+1]
- Beelzebub (19)
- Roper (19)
- Jorou-Gumo (19)
- Salamander (19)
- Arachne (18)
- Leanan Sidhe (18)
- Apophis (17)
- Karakasa-Obake (17)
- Chimaera (17)
- Slime (16)
- Cockatrice (16)
- Lesser Succubus (16)
- Dark Angel (16)
- Girtablilu (16)
- Dark Matter (16)
- Bicorn (16)
- Pharaoh (16)
- Kejourou (16)
- Jabberwock (16) [+1]
- Golem (15)
- Centaur (15) [+1]
- Mandragora (15)
- Wurm (15)
- Cancer (15)
- Liliraune (15)
- Devil Bug (14)
- Wererabbit (14)
- Dark Slime (14)
- Hobgoblin (14)
- Kitsune-tsuki (14)
- Kraken (14)
- Mindflayer (14)
- Black Harpy (13)
- Mermaid (13)
- Dryad (13)
- Large Mouse (13)
- Mummy (13)
- Skeleton (13)
- Grizzly (13)
- Blue Oni (13)
- Cheshire Cat (13)
- Hinezumi (13)
- Ren Xiongmao (13) [+1]
- Will-o-the-Wisp (13) [+1]
- Undine (12)
- Dark Valkyrie (12)
- Giant Ant (11)
- Gargoyle (11)
- Goblin (11)
- Scylla (11)
- Merrow (11)
- Sandworm (11)
- Mothman (11)
- March Hare (11)
- Cait Sith (11)
- Cupid (11)
- Red Slime (10)
- Hornet (10)
- Fairy (10)
- Kappa (10) [+1]
- Sphinx (10)
- Sylph (10)
- Parasite Slime / Slime Carrier (10)
- Honey Bee (9)
- Imp (9)
- Giant Slug (9)
- Sea Slime (9)
- Queen Slime (9)
- Charybdis (9)
- Ignis (9)
- Gnome (9)
- Kitsune-bi (9)
- Arch Imp (9)
- Dormouse (9)
- Akaname (9)
- Bubble Slime (8)
- Ant Arachne (8)
- Kesaran Pasaran (8)
- Dwarf (8)
- Khepri (8)
- Familiar (8)
- Troll (8)
- Shoggoth (8)
- Werebat (7)
- Jinn of the Jar (7)
- Lava Golem (7)
- Gandharva (7) [+1]
- Demon (7) [+7]
- Matango (6)
- Kakuen (6) [+1]
- Apsara (5)
- Houri (5) [+1]
- Wendigo (5)
- Kobold (5) [+1]
- Barometz (4)
- Soldier Beetle (4)
- Mucus Toad (4)
- Titania (1) [+1]