Just bought Hotline Miami; starting the installer, i realized you can't use anymore the "GOG.com" folder name as a destination, because of the "." in the name.

This would not be a problem per se, if not for a minor detail:
it was the suggested name of all the previous setup packages, which means that i already have all my GOG games installed there (on a dedicated partition, btw)

Why are you enforcing a different path now?
"GOG.com" is a pefectly viable folder name both in Windows and the good old DOS environment (Mac OS too, i think), and it 's really annoying now to have to split the games between two folder for no reason.
I could rename the old folder but that means i would have to double check all the config/registrry entry of each native Win32 game to be sure it does not mention that specific path anywhere.

Yes, it's an OCD issue, but still...

/end rant

Ah, I see you've just met the 2.x installers. There are ways to go around it, but main reason is that quite a few games disliked the period (and other characters), thus GOG.com found it prudent to change the default installation path.
Symbolic Links are your friend though.

Are you sure it doesn't work anymore?

I have just downloaded the Duke Nukem 3D installer (Arcanum installed in the GOG.com folder) and could install it
in the GOG.com folder.

No it isn't.

Not all of them got upgraded to the new installer. The old one has the green line made up of a bunch of vertical bars. The new one has a solid blue line.

True, I think it's an OCPD, but most people know of OCD and think it's the same.

Strange...

The GOG homepage states that the Duke Nukem 3D installer is version 2.0.0 .

Lots of people bitched about this, so at one point they took the limit away. All the newer 2.0 installers won't have the limit. All the "older" 2.0 installers will probably still have it.

Ya, I was having games show up in four different locations. I tried moving them all to one folder, but now their shortcut disappeared and I don't see the executable any more.

To me "GOG.com" was better than "GOG Games". Personally though a folder without a "." or a " " would of been best if changing it, aka "GoG".

Do symbolic links work (the windows shortcut files) for this? I'd of thought you'd need a "hard link" aka NTFS Junction:
junction.exe "C:\GOG.com" "C:\GOG Games"

Hmm... I had never even heard of OCPD until this morning. All I knew was OCD. Guess I learnt something, thanks!

Symbolic Link, Soft Link, Hard Link, similar concepts, slightly different things. I think (but not sure) that Soft Links are used for directories while Hard Links are used for files, but the idea is still the same. Treat directory A as directory B.
Best chance for info would be trying to find how the steam games could be installed in another drive, since that also required a link (soft or hard).

So... you can change your folder name with GOG games to GOGcom or become a heroin junkie.

I don't think there are other solutions.

Some people like crack. <,< >,>

But GOG is DRM-free! There is no crack!