Thanks for those
I've added Extreme Assault and Elemental series and found a list of Blue Byte stuff to look through at the bottom of its Wikipedia entry:

http://en.wikipedia.org/wiki/Ubisoft_Blue_Byte

I can't work out whether I consider Game, Net & Match/Great Courts series to be 'licensed' or not - descriptions seem to mention real world tournaments like The Davis Cup and there were [player endorsements in some territories
Hmmm...

The Square Enix sale made me realise that GOG has Conflict: Desert Storm so I removed 'Conflict Series' - Oops!

Ok I went through that Wikipedia list of Blue Byte games and added what I could to the Ubisoft list
Chewy: ESC from F5 is listed on Mobygames as being in the 'licensed games' category but I couldn't find any reference to Chewy the Outrageous Alien in any other context so I assumed this was a mistake and added it

Yo! Joe! Beat the Ghosts! seems to have been a co-publication between Blue Byte's 'Play Byte' label and Hudson Soft who's right will have ended up a Konami, added it with a note

looked more into the tennis games and Great Courts 2 definitely has you play the 'Davis Cup' - you have to pay someone to include the Davis Cup in your games, right? Therefore still classing them as licensed...

There doesn't seem to have been a PC version of Twinworld

Atomino seems to have been the only Blue Byte game published by Psygnosis, who's rights seem to have ended up at Sony so didn't include that one

OK Synced the Ubisoft list with what is available on Steam now
Even though I don't usually exclude licensed soundtrack games, I have decided that Rocksmith, Rock Band and Guitar Heroes are too reliant on their music licensing to be included

Bravo for the list, man!

OK added 3D Realms / Apogee and added all the titles on the 3D Realms site, including freeware titles
As they actually still appear to be available to buy on the 3D Realms site, I felt I had to include the Commander Keen series and Wolfenstein 3D even though they are on Steam as id / Zenimax
Noted it all though

Had Prey on the list for a bit but it was published by 2K / Take-Two like Max Payne 1 and 2 when I looked into it further
Prey is no longer on Steam, BTW!

I've now found 3 games to add to a 'Wadjet Eye' section
I didn't include Emerald City Confidential because its published by PlayFirst rather than being self published and I'm not sure that Wizard of Oz mythos is properly public domain

From 'changes' section:
"2013-09-12
Removed "Memoria (Daedalic)" (and now empty Daedalic section) as GOG released it today "

Giana Sisters: Twisted Dreams – Rise of the Owlverlord by Black Forest Games will come to GOG but isn't here yet. :-) Not sure if that counts as "missing".
It can be played as a stand-alone game or be added to Giana Sisters: Twisted Dreams.
Also Ravensdale backers will get it for free. :-)

Isn't The Cave IP owned by Sega, rather than Double Fine? I think its case is comparable to Emerald City Confidential, which you excluded from the list.

Oh yes, well spotted - that certainly explains why it hasn't turned up yet!
Removed (as as the Double FIne section as then empty - removed that to!)
Hi Piranjade
This thread is for completely missing series, Damien keeps a separate list for missing entries within a series, I have re-reported this missing expansion over there
http://www.gog.com/forum/general/completionists_list_of_missing_games_from_gog_series/post247
I'm really interested in his list too though so thanks for pointing this one out!

Well... I have some interesting ones. These are considered "missing" even if a) they are licensed, b) they haven't had any of them rereleased on GOG, and c) they never got a PC release, ever. (Here's hoping they change that! Especially with freaking DARKSTALKERS)

Capcom:
Darkstalkers (http://en.wikipedia.org/wiki/Darkstalkers)

EA:
Amnesia (this came out WAY before Amnesia: The Dark Descent, and was EA-original from what I can tell): [url=http://en.wikipedia.org/wiki/Amnesia_(video_game]http://en.wikipedia.org/wiki/Amnesia_(video_game[/url])
Need For Speed (Yeah yeah I know this is technically "licensed" because of all the licensed card but I want to see NFS, especially the older NFS titles, on here): http://en.wikipedia.org/wiki/Need_for_speed
Archon: The Light And The Dark: [url=http://en.wikipedia.org/wiki/Archon_(video_game]http://en.wikipedia.org/wiki/Archon_(video_game[/url])
The entire Burnout series
Earl Weaver Baseball (technically it's licensed because of the late Earl Weaver, famed Orioles manager, and the names of the players in the game, but other than that it is NOT licensed, and technically hasn't had another entry for quite some time that has been readily available): http://en.wikipedia.org/wiki/Earl_Weaver_Baseball
James Pond (how on God's green Earth did you guys miss this one?): http://en.wikipedia.org/wiki/James_Pond
The _____ Strike games (Desert Strike, Jungle Strike, etc.): http://en.wikipedia.org/wiki/Strike_series
Mail Order Monsters (fairly straightforward): http://en.wikipedia.org/wiki/Mail_Order_Monsters
Pinball Construction Set: http://en.wikipedia.org/wiki/Pinball_Construction_Set
Racing Destruction Set: http://en.wikipedia.org/wiki/Racing_Destruction_Set
Realm of Impossibility: http://en.wikipedia.org/wiki/Realm_of_Impossibility
Rock Band: http://en.wikipedia.org/wiki/Rock_Band

... Aaaaand just about everything else from when EA didn't flat out suck.

Yep all that seem to check out - added, thanks!

OK but personally I'm not including anything that IS licensed or never received a PC version / port
Darksiders - nothing in this series has a PC port
Amnesia - Added! (Maybe I originally thought it was based on a Thomas M. Disch novel and not an original work by him?)
NFS - Yeah licensed cars, I won't include it on this list
Archon - interesting - there was a PC version of the original Archon Published by EA but no PC version of Archon 2 then Archon Ultra, still developed by FreeFall was Published by SSI which would be Ubi Soft now - added both to their respective sections! (THEN theres Archon Classic by React games over on Steam too http://store.steampowered.com/app/65400/)
Earl Weaver - yeah, no sport's person fronted games in my list, sorry!
James Pond - only the 2nd one in the series made it to PC and the publisher for the PC version is listed in most places as Millennium Interactive Ltd. which ended up with Sony, sadly
Desert Strike et al - yeah, I've got them already, they are listed under 'S' for Strike Series
"Strike series (Desert Strike, Jungle Strike etc) (Ocean - EA) "
Mail Order Monsters - Never heard of that one, looks interesting but only came out for C64 and Atari 8-bits
Construction sets - Looks like Racing Destruction sadly didn't get a PC release but the 3 other 'construction sets' did - added this entry "Construction Set series (Adventure, Music and Pinball) (EA)" (not sure is the music one can even be considered a game but hay ho)
Zombies aka Mike Edwards Realm of Impossibility didn't get a PC release
Rock Band - I've said before that I'm not including Guitar Hero, Rock Band and games of that genre because they rely so heavily on the licensed music, sorry!

Thanks for the ones that made it onto the list!