How about some doujin games on Steam? (These are broken out by developer/circle
Orange_Juice:
100% Orange Juice: 102,399 ± 18,306
QP Shooting - Dangerous!!: 5,973 ±4,422
Suguri: 8,533 ±5,285
Acceleration of Suguri X-Edition: 8,533 ±5,285
Platine Dispositif:
Bunny Must Die! Chelsea and the 7 Devils: 22,186 ± 8,522
Gundemonium Recollection: 36,693 ±10,960
GundeadliGne: 38,400 ± 11,212
Hitogata Happa: 38,400 ±11,212
Edelweiss:
Fairy Bloom Freesia: 145,065 ±21,787
Astebreed: 71,679 ±15,317
Ether Vapor Remaster: 49,493 ±12,728
Astro Port:
Gigantic Army: 71,679 ±15,317
SATAZIUS: 44,373 ±12,052
ARMED SEVEN: 853 ±1,671
SITER SKAIN:
RefleX: 35,840 ±10,831
KAMUI: 26,453 ±9,306
ALLTYNEX Second: 24,746 ±9,001
EasyGameStation:
Recettear: An Item Shop's Tale: 383,143 ± 35,389
Chantelise: 160,425 ± 22,910
773:
Cherry Tree High Comedy Club: 86,186 ±16,795
Cherry Tree High I! My! Girls!: 48,640 ±12,618
Yakiniku Banzai:
War of the Human Tanks: 34,986 ±10,702
War of the Human Tanks - ALTeR: 853 ±1,671
Tennen-sozai:
eXceed 2nd - Vampire REX: 57,173 ±13,680
eXceed 3rd - Jade Penetrate Black Package: 58,026 ±13,782
The following circles/developers only have one game on Steam each:
Studio Pixel -- Cave Story+: 684,367 ±47,265
Smoking WOLF -- One Way Heroics: 224,425 ±27,094
NIGORO -- La-Mulana: 162,132 ±23,032
Tomoaki Sugeno -- Vanguard Princess: 153,599 ± 22,418
Petit Depotto -- Unholy Heights: 122,026 ± 19,983
Lizsoft -- Fortune Summoners: Secret of the Elemental Stone: 117,759 ± 19,631
Zenith Blue -- Mitsurugi Kamui Hikae: 108,372 ±18,832
Flat Software -- eXceed - Gun Bullet Children: 60,586 ± 14,082
Xtal Sword -- Eryi's Action: 50,346 ± 12,837
TORaIKI -- 99 Spirits/Tsukumogami: 43,520 ±11,936
Fly System -- Magical Battle Festa: 32,426 ± 10,303
Cross Eaglet -- REVOLVER360 RE:ACTOR: 30,720 ±10,028
souvenir circ. -- Croixleur Sigma: 26,453 ±9,306
YOTSUBANE/Adventure Planning Service -- Crimzon Clover WORLD IGNITION: 26,453 ±9,306
NEXT-SOFT+ -- Rime Berta: 21,333 ± 8,357
Dracue, Co. ltd -- Armored Hunter GUNHOUND EX: 10,240 ± 5,790
AlphaNuts -- The Sacred Tears TRUE: 7,680 ±5,014
(This isn't counting the multitude of visual novels on Steam now. Someone else can touch that fluffy tail.

)
Damn, that's quite the spread, and kind of impressive given that the majority of the games were done as hobbyist projects on the side. I'm willing to bet that almost all of these games have sold more on Steam than they ever did when originally released, when you can only buy them at doujin markets or at some specialty stores on consignment. One thing that can deflate those numbers (a little or a lot) is that almost all of these games have been sold in one or more bundles, either on Steam itself (like the Gundemonium and eXceed bundles) or on other sites. Heck, La-Mulana and QP Shooting are on Humble Bundle
right now. I really wonder how much that skews the numbers. I suspect you could probably figure that out a bit by comparing the percentage of owners with no playtime versus a normal retail release, but that would only give a rough approximation.
And yes, GundeadliGne/Hitogata Happa and Croixleur Sigma/Crimzon Clover are reporting identical numbers in SteamSpy.