They are in a standard format (iso or bin/cue).

I have run into problems modding DOSBox games from GOG so certainly see the problem here.

Maybe they don't retroactively add the missing setup/install/setsound to those games which miss them (like Ultima Underworld 1-2, Wing Commander games etc.), but it seems newer classic releases have them.

For instance the recent Willy Beamish release (a Dynamix/Sierra game) has an option to run the sound setup right in the menu, and I recall some other pretty recent GOG DOSBox releases having even a link to the sound setup right in the Start menu.

So it appears GOG has listened to its customers. It would be nice to have them back also for older GOG releases, but I guess I can manage as long as I can change them some other way:

https://www.gog.com/forum/general/music_and_sound_effects/post2

That's one way to look at it, personally I think they just don't care and have no guidelines in the office as to how a game should be delivered.

I always find it a nice extra if the full cd image is included, but that's secondary as long as the setup tools are included and the cd audio tracks are not lossy compressed. Sadly even this is not always the case.. Didn't they also use to provide cd audio for one or two of the Alone In The Dark games in a lossless format but then downgrade it to mp3 later? Unacceptable.

As for running the games in Linux; as already stated you don't need to re-install them, just edit the dosbox configuration a little bit and it's good to go.

Well, GOG in theory could just add a <100 Mb repacked bonus version for people who cannot download 700Mb.
Also, they could use .flac instead of the crappy .mp3

And I'm totally against the removal of the original setups and installation data too.

To me it seems they care, as their newer DOSBox releases seem to include e.g. the sound setup utilities. Maybe their guidelines have changed or become more detailed then.

It depends on the publisher, is my understanding. For instance, as Grargar has pointed out before, Activision games are all Windows-only titles, despite an abundance of DOS games from them. Did you ever let a bluetext know this like Judas or sent a message to Support (gave them a list of games that you own with this problem)? Worth a shot.

Fair enough, Screamer is a peculiar example then, as far as I can tell. GOG appear to use compressed audio in all their newer releases, I actually learned about cue files and how to use them with DOSBox from GOG titles. I guess they hadn't started doing that yet, when Screamer was released, but already had the (in my opinion commendable) philosophy of getting rid of redundant data.
Admittedly I did not and never really thought of doing so because the reason anyone would need Wing Commander's setup files is MT32 support which, let's be honest, at least 99% of all users would achieve illegally by downloading the necessary ROMs somewhere (and the same kind of user shouldn't have any problems or qualms getting the corresponding configuration or setup files either).

true, while a bit annoying, this would work.
however, i feel a non-modified ISO (at least in this case, where the space savings are minimal) is very much preferred by me. an unmodified ISO would have more advantages, you could actually burn it and run it on an old machine, you could easily run it in emulators other than DOSBox, and all in all would be a bit more future-proof. thinking as the game copy as a digital archive, i really want things to be as original as possible.

The point is that GOG could just offer both options.
Then they'll be able to check the stats themselves to understand what the majority really wants.

FLAC compresses at ~40-50%
MP3 compresses at ~90-95%
128 kbps Mp3 music is usually noticeable vs a well recorded uncompressed track (if you have a good sound system).
With ~50% difference, you'd be able to get the 100% original.

Let's not only offer worsened versions for everyone in 2017..
It's like with those folks who still settle for DVDs.. let's not stop offering BDs just because they don't need\can't afford better resolutions.

You can check some reasons on Wikipedia. O_o
Obviously none can be considered absolutely perfect, but they're not exactly random either.

The "50%" don't make any sense. Let's be generous and compare 50% FLAC versus 90% MP3. That makes FLAC 500% the size of the MP3 version. Now let's say 40% FLAC versus 95% MP3. That makes FLAC 1200% the size of MP3. That's pretty darn relevant, especially in the context of old games where the audio music comprises the vast majority of the data.

You don't even need particularly good hardware to notice the quality difference between 128 kbit mp3 and a FLAC file, it's just that there's almost no chance that the quality difference will be relevant to the gameplay experience. Just to be safe I would personally settle for 192 kbit, though, due to the risk of highly noticeable artifacts in high-pitched noises at 128 kbit.

Soundtracks offered as bonus content are an entirely different matter and I would get legitimately mad if those were offered as puny 128 kbit mp3s. I still wouldn't go as far as requesting FLAC's, though.

I never said GOG should only offer downscaled versions, I just said that the standard release should shed redundant data and use compression of CD audio tracks to reduce download and installation size. However, I DO want GOG to include lossless CD images as bonus content.

You surely know that the standard was established by Sony in the context of the development of the CD. The audio quality was imposed by desired playtime (at least to some degree influenced by Norio Ohga's personal preference), physical size (which in turn was imposed by certain economic factors and compatibility with existing hardware), density / reliability (desired by the engineers) and of course the coding technology available at the time which was developed and changed until the very last moment the CD was officially introduced (quite a random factor, wouldn't you say?). All in all it can be summed up as one big clusterfuck that eventually had to result in a finished product.

Now, there was of course a scientifically founded minimal quality that had to be achieved but that minimal quality still made certain assumptions about the hearing range of the average human (20hz to 20khz). Assumptions similar in nature to the ones made during the development of the mp3.