Dungeon Keeper on GOG only includes the manual for the vanilla game, and not for the Deeper Dungeons expansion. I checked, and the expansion does indeed have a separate manual:
[url=http://www.ebay.com/itm/PC-DUNGEON-KEEPER-THE-DEEPER-DUNGEONS-INSTRUCTION-MANUAL-ONLY-FREE-SHIPPING-/391449692161?hash=item5b24384801:g:LZEAAOSwn9lXK5CO]http://www.ebay.com/itm/PC-DUNGEON-KEEPER-THE-DEEPER-DUNGEONS-INSTRUCTION-MANUAL-ONLY-FREE-SHIPPING-/391449692161?hash=item5b24384801:g:LZEAAOSwn9lXK5CO[/url]
But I can't find it in pdf form.

However, there is also a separate manual for Dungeon Keeper Gold (vanilla + expansion) which can be downloaded here:
[url=http://dungeonkeeper.wikia.com/wiki/File:Dungeon_Keeper_Gold_-_Manual_-_PC.pdf]http://dungeonkeeper.wikia.com/wiki/File:Dungeon_Keeper_Gold_-_Manual_-_PC.pdf[/url]

Technically, only the Gold manual should be included on GOG because that's the version GOG is selling, so that's what I'm adding to the list. However, I'm really curious on what's included in the Deeper Dungeons manual (and whether it has any additional info not available in Gold manual), so if anyone finds a copy, I'd be really grateful. Thanks.

Thanks for letting me know about that one. I compared the 2 manuals a bit (I own DK Gold since it was given away on 2014) and the one of the Gold Edition seems to have the exact same contents as the vanilla one, minus a FAQ in the beginning. I included it in the gogmix anyways though, just so that people know... As for Deeper Dungeons, it seems it was mainly an addon of new missions and a fix of the AI and the few more new features mentioned in the mobygames description are probably some other minor changes, which might or might not be documented in that separate manual.

Yes, I'm thinking the Gold manual simply combined those two manuals verbatim, which would mean that Deeper Dungeons manual is exactly those several extra pages at the beginning (which is reinforced by the fact that the section ends with Credits, something that's usually put at the end of a manual). The only thing, it's difficult to say but in the ebay listing it looks a bit thicker, so I'd be happy if anyone who actually owns a manual can confirm.

Dungeon Keeper also came with a reference card that's mentioned in the manual, but not included with GOG. The only information I found, are the shortcut keys in this thread.
https://www.gog.com/forum/dungeon_keeper_series/wheres_the_reference_card_for_dungeon_keeper_gold

Not sure if you want it in the GOGmix, Treasure, but for completeness sake, I'll include in in the list.

I am sorry if this is not worth adding, but while the original Europa Universalis does have a manual included with the GoG installation, the Table of Contents is missing (which is a problem for a 150+ page manual for a grand strategy game).

There was a replacement linked to on the Paradox homepage, but it has since been removed. I have contacted their support and will update this post if they re-upload it.

Do you have a link to the old page? Maybe there is a cached/archived version?

I don't know, I personally usually don't find shortcut keys in games terribly useful as someone might change the controls and then the shortcut keys might be different and whatnot. I'll leave it out of my gogmix atm and see in the future...

That webpage might not be needed, as the version of the manual found in replacementdocs includes the table of contents - only difference is it does not have the alphabetical index that's at the end of the version gog gives, but the rest of it is very accurate down to the page numbers. For this reason, I made the toc pages a separate pdf uploaded on Google Drive -needless to say, I'll give an entry for that, because I like having a toc in my history books, and manuals for grand strategy games have many similarities with real deal history books.

Could you please upload the GOG version somewhere so I can compare?

Sure. Here you go:

https://drive.google.com/open?id=0BwpXI6_1f1OQcWhMUVkxZG4wWU0

I personally own the game as I think I got it in a bundle in a summer sale (probably last year's sale), and I kind of forgot that not everyone would own it....

Thank you. I'll link to the whole one on replacementdocs in my list too. It's weird that that one doesn't have the index that GOG does have. Wonder how the physical one looked like. Or perhaps some versions come with TOC, while others with Index.

Regarding the Dungeon Keeper reference card, Paradoks has kindly scanned his Polish version. Still waiting for the English one, but in the meantime you can more or less see what was included in it, besides the shortcut keys. Most of it was lots of (mostly outdated) technical stuff, as well as multiplayer info.

You can take a quick look at it here:
https://www.gog.com/forum/dungeon_keeper_series/does_anyone_have_the_reference_card_for_dungeon_keeper_1

It's enough to make it to my list, but probably not to your GOGmix. Make the decision yourself anyway as you wish.

Titan Quest is now in the house! It doesn't include a manual in the extras though...
I found manuals for both the basegame and the Immortal Throne expansion, and I'll post their links here for the moment, since Gog hasn't included the game in the gogmix selection pool yet for some reason...

Basegame: http://cdn.akamai.steamstatic.com/steam/apps/4540/manuals/TQManual_US.pdf
or (prettier version)
http://www.replacementdocs.com/download.php?view.4487

Immortal Throne: http://cdn.akamai.steamstatic.com/steam/apps/4550/manuals/TQIT_Manual_EN.pdf
or (prettier version)
http://img.metaboli.fr/products/19909999/en/user_manual.pdf

Btw, the full changelog as posted by Nordic's ThomNG in the release thread indicates that the 2 games were merged in one -I wonder how that affects the manuals...

Given this new data, the manual of the Gold edition (here: http://www.manuals.nordicgames.at/files/TitanQuest/TitanQuest_Gold_PC_Manual_EN.pdf) might be a good fit as well...

^^
Thank you.

Oddworld: Munch's Odyssey was released today, and it also doesn't come with a manual. If I understood correctly, this version is a port -of either the Xbox version or the Android one. I saw that a person on the Steam forums took the Xbox manual and adapted a bit (e.g. by including the pc controls) and uploaded it in Dropbox.
The thread: http://forums.steampowered.com/forums/showthread.php?t=1673426
The manual: http://dl.dropbox.com/u/7756245/Munch%20PC%20Manual.pdf

These were posted in 2010 though, so there might be some differences between the 2010 Steam version and the 2016 gog one...

In case you're curious, here's the original Xbox manual: http://www.replacementdocs.com/download.php?view.1397

I was thinking something since yesterday:
Shadow Warrior Classic Redux was released yesterday, but it doesn't include a manual. The only difference I see between the Redux and the Classic Complete would be the visuals - the gamepage does mention "two massive expansion packs" being present, but the Steam page of the game clarifies that those two are "Wanton Destruction and Twin Dragon (OpenGL)" which means that those are the same included in Classic Complete.
->In short, the Redux of Shadow Warrior doesn't include the manual, but I suppose people can use the manual given with Classic Complete, which is easy to acquire since that game is now free.
I'll put the mention in my gogmix just so it is there for people to see...