Formerly free games that were turned into paid-for? (STEAM)

Organ trail?

You can play a pretty limited but very experiential version of The Stanley Parable (mod not standalone) on steam for free. It's great if the demo just wasn't enough and you need to know more about what isn't going on..

Counter-strike, Dear Esther, Killing Floor, Stealth Bastard, Cave Story

APB RELOADED PREMIUM PACK? Ty.

It is not steam but HoN was free during beta,then they went pay2play and then later again free...ooohhh S2 /facepalm

I don't have an answer to your Q but I can try to give you a list of games that fit the category you're speaking of:

Aether -> (included in The Basement Collection)
Ballads of Reemus: When the Bed Bites (free to play online) -> (same title)
Ben There Dan That -> (same)
Bestowers of Eternity -> The Blackwell Legacy
Cart Life -> (same)
Cave Story -> Cave Story+
Closure -> (same)
Coil -> (included in The Basement Collection)
Crayon Physics -> Crayon Physics Deluxe
Desktop Dungeons -> (same title with DLC)
Dino Run (ftp online) -> Dino Run SE
Epic Battle Fantasy 4 (ftp online) -> (same)
Eversion -> (same)
Evoland (pixeljam) -> (same title, includes pixeljam version)
Frogatto & Friends -> (same, greenlight)
Grey Matter -> (included in The Basement Collection)
Haunt the House (ftp online) -> Haunt the House Terrortown (greenlight)
Hexagon -> Super Hexagon
Home Sheep Home 2 (ftp online) -> (same)
Kingdom Rush (ftp online) -> (same)
La-Mulana -> (same)
McPixel -> (same)
Meat Boy -> (included in The Basement Collection, same title)/Super Meat Boy
Mirror Moon -> Mirror Moon EP
No Time to Explain -> (same)
Orbitalis -> (same)
Postmortem: One Must Die -> (same)
The Shivah -> (same)
Soundodger (ftp online) -> Soundodger+
Speedrunner -> Speedrunners
Spelunky -> (same)
Spewer -> (included in The Basement Collection)
Stealth Bastard -> Stealth Bastard Deluxe
Super House of Dead Ninjas (ftp online) -> (same)
Super Puzzle Platformer Plus (ftp online) -> Super Puzzle Platformer Deluxe
Surgeon Simulator 2013 (ftp online) -> (same)
Tales of Maj'Eyal -> (same)
Time Fcuk -> (included in The Basement Collection)
Treasure Adventure Game -> Treasure Adventure World (greenlight)
Triachnid -> (included in The Basement Collection)
Windosill -> (same)

Bonus: These aren't the same games but are included for honorable mention
Narbacular Drop -> (inspired) -> Portal