Since I'm used to having tons of different client-programs and installers, in the options w/in the program or upon install w/ installer files, I usually put them all by what service it requires (most important to me) or where I bought them from (secondary - usually used if a service like Steam or Origin is NOT required).
This is not 100% the exact paths I use, but you get my drift...
It makes it SO MUCH easier, for me to know where I bought what; what game uses or requires what program; etc etc.
This also helps me not get patch types mixed-up (Steam version patches are usually different from Non-Steam versions) and other things...
Examples:
Steam-required or Steam-purchased games go in Steam folder (no choice in the matter, actually)
EA Origin-required, games bought from Origin, or EA games go in say C:\Program files (x86)\Origin Games
Amazon Download purchased games go to say C:\Program files (x86)\Amazon Download Games
Games bought from G4WL games go in say C:\Program files (x86)\G4WL Games
GreenManGaming games go in C:\Program files (x86)\GMG Games
Games bought from GOG games go in say C:\Program files (x86)\GOG Games
Retail games (usually w/ disc-check based DRM or NO DRM from retail) go in say C:\Program files (x86)\Retail Games
GameFly games go in say C:\Program files (x86)\GameFly Games