Here you go
Quake (original retail manual)
https://drive.google.com/open?id=1NMQ4dAogi-wEBEyFlaaKA1hvgNX1oenV

Thank you. That's one game off Appendix A.

The Animation Arts collection of point-n-click games (Secret Files series + Lost Horizon series) was released a couple days ago, but they don't have any extras - and hence, neither manuals separately included as extras either. Here's the situation regarding the manuals for each game:

-Secret Files: Tunguska
The manual is available inside the game's installation directory (as found via right-clicking the desktop shortcut > Properties > Open file location), called Manual.pdf. Haven't otherwise found a copy online.

-Secret Files 2: Puritas Cordis
Haven't found a copy online, but given the situation with Tunguska, highly probable it is in the game's installation directory -needs confirmation, since I haven't downloaded the installer.
Update: The manual is available inside the game's installation directory - confirmed by Pajama (see below)

-Secret Files 3
Manual found online at https://steamcdn-a.akamaihd.net/steam/apps/216210/manuals/SF3_Manual.pdf. Also, given the situation with Tunguska, highly probable it is also in the game's installation directory, but needs confirmation, since I haven't downloaded the installer.
Update: The manual is also available inside the game's installation directory - confirmed by Pajama (see below)

-Secret Files: Sam Peters
Haven't found a copy online, but given the situation with Tunguska, probable it is in the game's installation directory - needs confirmation, since I haven't downloaded the installer.
Update: The manual isn't in the game's installation directory either (confirmed by Pajama - see below), so it is still missing....

-Lost Horizon
Manual found online at https://steamcdn-a.akamaihd.net/steam/apps/40350/manuals/LH%20Manual%20UK.pdf. Also, given the situation with Tunguska, highly probable it is also in the game's installation directory, but needs confirmation, since I haven't downloaded the installer.
Update: The manual isn't available in the game's installation directory, so the link I provide here is the place to get it from.

-Lost Horizon 2
Haven't found a copy online, but given the situation with Tunguska, highly probable it is in the game's installation directory - needs confirmation, since I haven't downloaded the installer.
Update: The manual isn't in the game's installation directory either (confirmed by Pajama - see below), so it is still missing....

I started playing the first Secret Files game already (which is how I know for sure that the manual is in the install directory), but will download and install the other games in order after I finish with this one, so if there's anyone else who installs and starts playing one of these other games, please confirm if there are manuals in the installation folders of the other Animation Arts games - done by Pajama.

P.S. In case anyone needs to contact me, I stopped participating in the gog forums (or any other forums, for that matter) since a year or more ago, so I normally sign in infrequently (maybe once a month or so). I check this thread however every now and then, and upon noticing that these games had no manuals and no one else had posted about it, decided to add my input on that. Obviously, now that I posted in here regarding the Animation Arts games, I'll stay tuned for any answers to my post.
In general, I think I gradually became disillusioned with GOG for various reasons, and now buy games from them only infrequently, if they are games I want a lot, are cheap and don't have exorbitant system requirements. I also started moving away from pc gaming in general, since I grew tired of having to constantly look at system requirements, and also of how more modern games require so much RAM and advanced graphics cards in order to be played. I bought a PS4 recently, and play more regularly there nowadays. I won't be moving from pc gaming completely however, since on one hand I have a lot of backlog on the pc (though I'm thinking of buying the PS4 versions of some of the games that are available for that as well - mainly the more graphically intensive ones), and on the other hand, consoles in general are severely lacking in some genres - point-n-click games being obviously one of them - and also with a console, one is limited to games either released in the last 4-5 years or remastered during that time span, and in order to play older not remastred games, one would need a different console, while on the pc - barring some games needing complicated compatibility measures - one can play games spanning many console generations.

Rightio, I've just checked and Secret Files 1-3 all have manuals which are installed when installing the game.

Secret Files: Sam Peters and Lost Horizon (both 1 and 2) do not have any manuals installed.

Thanks for finding the missing LH manual, now have it downloaded :)

Thank you for providing this information. Updated my post accordingly, so that this info is all in one place.

Thanks. I'll add to the main post in a bit.

Stranglehold was released earlier today, but it doesn't include a manual in its extras. The manual can be found at http://www.replacementdocs.com/download.php?view.5965.

Red Faction: Armageddon is missing its manual. It can be found in the link below in English, French, German and Spanish:
https://manuals.thqnordic.com/?dir=RedFactionArmageddon

In addition... I was able to find the manual thanks to Wayback Machine and I have uploaded it to my Dropbox:
https://www.dropbox.com/s/fygg767rqa4403r/Munch%27s%20Oddysee.pdf?dl=0

Thanks both. Sorry I haven't updated this yet.

Everything now is up to date.

The manuals of a few of the recently released games seem to be missing (at least by glancing to see if there are goodies sections including them). Here's the situation:

-Arabian Nights: The manual seems to be missing. It is at https://www.popuw.com/files/Arabian_Nights.pdf
-Hexplore: The manual seems to be missing. It can be found inside the game folder and also online at http://www.replacementdocs.com/download.php?view.6930.
-Submarine Titans: The manual seems to be missing. A really detailed manual can be found at https://archive.org/details/Submarine_Titans_Manual.

Since the manuals might not be noted as extras, but might be present in the game folder, please verify if the manuals of the aforementioned games are also in the game's folders or not.

According to SCPM, this one is in the game folder.

Thanks for letting me know. Updated my post accordingly.

All updated. Thanks.