Grargar: Nosferatu: Wrath of Malachi seems to have a manual (as shown [url=http://www.ebay.com/itm/Nosferatu-The-Wrath-of-Malachi-PC-2003-/252312925608?hash=item3abf05b5a8:g:OVMAAOSw5IJWgjEu]here[/url]), but it's not available on GOG, ReplacementDocs or on other digital stores.
Added
Treasure: -
Raven Legacy of a Master Thief: I know for certain that this one has a manual because I own its retail version (I haven't played it yet, but that's another story...) However, owning the printed manual is one thing and scanning it and uploading it wherever is another -its the scanning part the tough one because I don't own a scanner. I should probably try and scan it some time or another though... Just so you know (and now that I'm commited to that in written format that might make it harder for me to forget to do so...)
Added. Thanks for the offer, though of course don't feel obligated to do it if it's not easy.
Added more stuff from the GOGmix.
Also, I decided not to include games if the manual can be found in the installation folder.
I've added a list of open questions for cases where I'm not sure if a manual existed in the first place (I usually check eBay to see photos of second hand copies that are being sold). If anyone knows a definite answer please let me know.