I was fortunate to buy The Chronicles of Riddick: Assault on Dark Athena on GOG - that game's been disappeared, and the DRM on the retail version and Steam version was awful.
There are a lot of games that disappeared over time that really should come back. Outrun 2006 got taken down like 14 years ago due to the Ferrari license expiring - I bought the retail version of that back when it first launched, so that's not a problem for me. Other stuff like Prey and Wolfenstein 2009 disappeared at some point (I can't remember if Wolfenstein came back). The one that's been bugging me recently is Gears of War - the original version, not the Ultimate Edition that changed a lot of the overall aesthetic. I really wish we could get that one back, as Games for Windows Live and whatever other DRM schemes really fucked that one over (remember the glitch that rendered that game inoperable back in 2009?) Games For Windows Live, like most things MS ever does on PC, really fucked a lot of games up.
Obviously, there are also still a lot of older games that never made the leap to digital distribution. I'd personally like to see Heavy Metal FAKK 2 make a return. My other, extremely random one I've been pining for is Earthworm Jim: Special Edition, which is the best version of the game but only available as a Windows 95 retail release that has some issues on modern machines.
This is all basically why I'm a GOG fanboy - if these sorts of games are ever going to make a comeback, it's because they seek it out. This shit just doesn't happen on its own at this point.