Total Annihilation comes with a manual for the base game, however there are no manuals for the expansions: Core Contingency and Battle Tactics.

Did these come with separate manuals?

I found some evidence on eBay that at least BT did:
[url=http://www.ebay.co.uk/itm/Total-Annihilation-Battle-Tactics-Expansion-Big-Box-PC-Game-/201559047880?hash=item2eeddafec8:g:OmgAAOSwSzdXCosy]http://www.ebay.co.uk/itm/Total-Annihilation-Battle-Tactics-Expansion-Big-Box-PC-Game-/201559047880?hash=item2eeddafec8:g:OmgAAOSwSzdXCosy[/url]

Nothing conclusive for Core Contingency. There are some photos of the box and CD case, but can't tell for sure if there is a booklet inside the case.

Could anyone who has the original physical games confirm?

Oh man, THANK YOU THANK YOU THANK YOU. This should be stickied, officially supported and kept up to date. Or, you know, gog should just get all the damned manuals.

Also, Battle Realms manual is fine, except that illustrations are of extremely bad quality. This is not a big issue mostly, but what could have been extremely useful appendices (tech trees and such) at the end become completely unreadable (see attachment).

I wonder if anyone has a better copy.

Just copying Treasure in case she wants to add Battle Relams to the mix. I found better copies of the appendices on Battle Realms wiki.
e.g.
[url=http://battlerealms.wikia.com/wiki/File:Battle_realms_bemutato_08.JPG]http://battlerealms.wikia.com/wiki/File:Battle_realms_bemutato_08.JPG[/url]

Compare this to the file attached in previous post or to the pdf manual if you have the game.

Not sure if it's enough to qualify adding to the GOGmix.

I do own said game, since it was given away in the summer sale of 2015. Seeing the manual, it appears that all pictures are of worse quality than the text, but only those on the pages 47 and 48 (Unit Alchemy and Structure Trees) are important enough. From your link I found the other tables that are blurred in the manual -here are the collected links:
Page 47
[url=http://battlerealms.wikia.com/wiki/File:Battle_realms_bemutato_08.JPG]http://battlerealms.wikia.com/wiki/File:Battle_realms_bemutato_08.JPG[/url] (Dragon Unit Alchemy)
[url=http://battlerealms.wikia.com/wiki/File:Lotus1.jpg]http://battlerealms.wikia.com/wiki/File:Lotus1.jpg[/url] (Lotus Unit Alchemy)
[url=http://battlerealms.wikia.com/wiki/File:Serpent1.jpg]http://battlerealms.wikia.com/wiki/File:Serpent1.jpg[/url] (Serpent Unit Alchemy)
[url=http://battlerealms.wikia.com/wiki/File:Wolf1.jpg]http://battlerealms.wikia.com/wiki/File:Wolf1.jpg[/url] (Wolf Unit Alchemy)
Page 48
[url=http://battlerealms.wikia.com/wiki/File:Dragon2.jpg]http://battlerealms.wikia.com/wiki/File:Dragon2.jpg[/url] (Dragon Tech Tree)
[url=http://battlerealms.wikia.com/wiki/File:Lotus2.jpg]http://battlerealms.wikia.com/wiki/File:Lotus2.jpg[/url] (Lotus Tech Tree)
[url=http://battlerealms.wikia.com/wiki/File:Serpent2.jpg]http://battlerealms.wikia.com/wiki/File:Serpent2.jpg[/url] (Serpent Tech Tree)
[url=http://battlerealms.wikia.com/wiki/File:Wolf2.jpg]http://battlerealms.wikia.com/wiki/File:Wolf2.jpg[/url] (Wolf Tech Tree)

I'm not certain if I should add these to the gogmix, but if I do, I'll have to consolidate these images into a single link (e.g. upload them to Dropbox or something) so that they'll fit in the character limit. I'll think about it...

I just noticed those files aren't exactly what is in the vanilla manual. They include units from the expansion.

Compare for example the file here:
[url=http://battlerealms.wikia.com/wiki/File:Serpent1.jpg]http://battlerealms.wikia.com/wiki/File:Serpent1.jpg[/url]
With the one that appears on page 47.

The Assassins' Den, Enforcer and Witch were all added by the expansion.

Not sure still if it's worth including to the "missing without replacement" list. Ideally we'd have a good quality Battle Realms manual, but then again even if these images aren't exact they do their job.

I might add them to my list. Hopefully soon I'll have time to sit to it, do a bit of restructuring and formalize inclusion criteria.

Huh, I see - I didn't notice the differences, what with the original pictures of the manual being blurry and all. On another note, while the quality isn't 10/10, it is rather good (maybe 8.5-9/10), in the sense that the text is both readable and selectable (via OCR presumably), something that can't be said for other manuals. You decide then on whether to include it on the OP or not -after all the game can still be understandable and playable even without those images, as the text by itself seems to be quite thorough.
In short, I don't think I'll add these to my gogmix, as the manual provided is of a rather good quality in every other aspect.

Well, finally had some time today to work on this a bit more. The list turned out larger than expected so had to do a bit of restructuring. The master list itself now spans three posts, while everything else was put into neat little appendices in the fourth post. I'm hoping it looks clear.

I hearby officially announce this list to be out of beta. It is now, to my knowledge, complete. And compatible with Treasure's GOGmix. Any differences between it and the GOGmix are mainly due to:

_ Treasure has more restrictive inlusion criteria. Generally, important gameplay information has to be missing to be included in it. Stuff like blurry pictures is no reason for inclusion.
_ GOGmix includes non-English manuals. This list only does if no English replacement is available.
_ GOGmix doesn't include non-PC manuals. This list does, if no PC replacement is available.
_ GOGmix doesn't include games for which the manual is missing, but no replacement is found (like Raven).
_ List only includes manuals that can be put as one file in the "extra goodies". Games for which the manual is a webpage, wikia, guide or similar (e.g. Shovel Knight) are not included.
_ List doesn't include manuals that are found in the game folder after installation. These are included in a separate Appendix instead.

And I've officially contacted GOG support about this. Hopefully they can include some of those manuals. Let's see what they reply. Maybe soon this list will grow smaller :).

Two things regarding Shovel Knight:

1) According to this page, the game does have a manual for the retail versions.
2) The game's Deluxe Edition offered via their site makes mention of a digital manual.

I think that it should stay on the list.

Thank you (and nice new avatar!).

The link in the GOGmix can't be the 46+ pages digital manual they talked about, especially since according to the second link you mentioned, that would come with the Deluxe version, which is more expensive. Not sure if GOG can add it in that case anyway with out selling a separate Deluxe version too.
Still, given that, it still should be added to the list, and to Appendix A too. EDIT: Added now.

As I mentioned previously, the Metro Redux games weren't sold separately on retail, but only as a bundle. Anyway, according to this unboxing video, the retail PC version doesn't have any manual and only seems to have an advertising booklet for the Metro novels, though I can't confirm if that's what also the speaker says, as I don't know Spanish.

Thanks, I was waiting for a confirmation for a PC version.

The newly added Sherlock Holmes games lack manuals in the extras. I found manuals for most of them (with the exception of Nemesis -will keep looking for that one) with one caveat though: The manual I found for Awakened is for the original, not the remastered. The differences between the 2 editions are detailed [url=https://en.wikipedia.org/wiki/Sherlock_Holmes:_The_Awakened#Remastered_Version]here[/url], just in case you're curious...

edit-ah wait, apparently, in most other territories the Nemesis game was rather released as Sherlock Holmes vs Arsene Lupin, and I thus found the manual of that one too, albeit the original and not remastered again (differences between the 2 versions)... Scratch that, luckily the manual I found is for the remaster indeed! Yay!

Thanks. Updated the list.