I'm thinking the introduction of the Program Files folder coincided with the advent of spaces in paths. Before Program Files you couldn't name a file "My File.txt" people did MyFile.txt or my_file.txt. It must've been one of the 9x but I can't remember.
Either Windows 95 or NT would be my guess...with NT came NTFS which supported long filenames (and spaces) from the start.
If I remember correctly 95, being DOS/FAT32-based, added some kind of extension to the FAT32 specification to be able to use long filenames too, but everything was still accessible through 8.3 names (first 6 characters plus tilde plus a number, usually 1 as in C:\PROGRA~1). Even NTFS still creates 8.3 names but that can be disabled for a tiny performance boost.
Anyway, I don't think the whole "Program Files" thing was around in Win3.1/3.11 days...Interesting question, though :)
I played around with NT 4 Server for awhile. I think the Operators User category was where they got the inspiration for an Administrator account that wasn't the full blown admin account they way they do it on Vista and W7 now. An Operator could install programs, register/unregister ActiveX/COM stuff etc.. but could not delete system files.
I tried it years after it was the current system. It ran quite smoothly on a Pentium III with 128 MB ram. The funny thing was there was no write caching since it was a server and it was thought that the data should be immediately flushed to disk. It was almost funny. Every time you wrote a file, even if it was a small text file, when you saved it you heard it write out to disk. Ah the good old days! :)
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