I have now installed my third GOG game on my computer using the installers that I downloaded,
e.g. into the subdirectories
D:\GOG\Firaxis\Sid Meier's Alpha Centauri
D:\GOG\MPS\COLONIZE
D:\GOG\Origin\Wing Commander 1 and 2

and have now several instances of DOSBOX installed e.g. in
D:\GOG\DOSBOX
D:\GOG\Origin\Wing Commander 1 and 2\DOSBOX
and the DOSBOX I already had before installing games from GOG in
C:\Programme\DOSBox

How can I prevent the installers of GOG to install yet another instance of DOSBOX?
And how can I get rid of the DOSBOX folders I already have (except one) without breaking the games that are installed?

When you're in the "main menu" of installation where there's an install button there's an option button as well. Press it and then you get to pick the game, dosbox or both and I think a PDF reader.

You can just have one DOSbox installed, but it's tiny and very convenient. So unless you're still struggling with a ludicrously tiny HDD I'd just carry on installing DOSbox with every DOS game you install.

You may choose not to install DOSBox with every game during installation.

Oh, that's too bad. I haven't noticed ;(

http://www.gog.com/wishlist/site/single_dosbox_install_for_all_dos_games

Someone over there mentioned versioning/compatibility concerns.