Actually, such a list/topic is a very good idea, IMHO.
Because it's not publicly known what criteria there are for games getting in/staying out of GOG catalog, at least such a list would give us outsiders a chance to find some common things with those rejected titles, if there are any to be found.
But for such a topic to be useful, it would be necessary to post some source, even if speculative, for that information. Just because some game isn't on GOG, it doesn't automatically mean that it has been rejected.
Anyways, I might begin with some games that I can recall, and hopefully others will follow.
The Uncertain Source: Kickstarter for episode 2.
"We tried to publish on GOG with Episode 1, but they wouldn't consider it somewhy. We will definitely try it with Episode 2 too but we cannot make any certain announcements as we don't know for sure yet."
http://www.kickstarter.com/projects/1321269974/the-uncertain-episode-2-light-at-the-end Tokyo Dark Source: Kickstarter for Tokyo Dark
"We know that a number of you are not fans of Steam and prefer to have your games completely DRM free. We are currently talking to platform partners to launch Tokyo Dark on, though this is going slowly and is unfortunately an area we have no control over."
http://www.kickstarter.com/projects/114971883/tokyo-dark/posts/1918692 Her Majesty's SPIFFING Source: Kickstarter for Her Majesty's SPIFFING
"Regrettably, things didn’t go smoothly with the distribution of download keys to backers either, which I feel the need to apologise for again. It transpired a small (but not insignificant number) of folks didn't receive the email containing their download key and, unfortunately, GoG ultimately decided that they didn’t want our game on their platform."
http://www.kickstarter.com/projects/billygoat/hm-spiffing-a-comedy-3d-space-themed-adventure-gam/posts/1864219