This is mostly fixed in the new 2.0.61 version. The Deals category is now GOG Store, and below that you can go directly to the homepage, All Games, and Deals. Search is still awkward, as it's a prominent UI feature and it's not apparent you're searching third-party stores, but at least you have the "Available on GOG.com" note and the View in Store button where applicable.

I also appreciate the download ETA and taskbar progress bar.

Thank you.

It would probably help if you'd stop removing owned games from people's libraries. I can't imagine it instills confidence. And no, I'm not talking about games being removed because they were purchased from a key reseller.

This is just what I took note of. It's probably not an exhaustive list.
Three kingdoms story: Conussia
Syberia: The World Before artbook
Alwa's Awakening
Metal Gear Solid games
The Elder Scrolls: Arena and Daggerfall -- hey, these are free, so who cares, right?

Edit:
Lords of Magic: Special Edition
Lost Eidolons
Bonus gift code for Impaler (and possibly other games)

Edit #2: pre-order bonuses not added to account
A Plague Tale Requiem: - Protector Pack DLC
Steelrising - Cagliostro's Secrets

Edit #3: time-limited launch bonus removed from account
Transport Fever 2 - Early Supporter Pack DLC

Edit #4:
X4: Foundations and various other games

Well I guess anyone would agree that this is very bad.

That one really grinds my gears and the examples are in the hundreds. It applies to every other bundle/deluxe version. BloodRayne games are probably the worst. I have bought a complete bundle TWICE from them for the sake of experimentation (BloodRayne Complete Bundle and then BloodRayne Absolute Bundle), yet none of the individual games are still marked as owned.

As you said, this goes the other way too. Owning all the contents of the bundle, does not mark said bundle as owned. Darksiders 3 Deluxe Edition, A Plague Tale Bundle, The Surge 1 & 2 - Dual Pack, Shooter Dual Pack - Necromunda: Hired Gun + Space Hulk: Deathwing - Enhanced Edition, etc. Steam certainly doesn't have such issues. Steam also grants an appropriate discount for a bundle when some of the contents of that bundle are already owned. Not GOG though.

While this broken ownership marker issue may not seem like a big deal, it renders the "Hide owned games" filter completely pointless on GOG.

Also while I'm on the topic of filters, I really wish there was a "Show only DLCs for owned games" filter, to make tracking down new DLCs much easier. Please vote for it here.

You can add "Lords of Magic: Special Edition" to the list! Source from german forum

It happened to me with Lost Eidolons, I only noticed as I went to buy a gift copy and instead it had the option to buy the game for myself.
In the end a blue had to gift me the game as a replacement.

I had this happen to me with The Elder Scrolls: Arena and Daggerfall. Good thing is was simple fix. This why I keep document with list of all my games and total number.

Oh it doesn't prevent anything, it only warns. The fact that the checkout page is aware of your ownership, while the store front is not, kinda implies that there's some sort of a duality to their database and that perhaps they should be merged. At the same time, there's probably next to no incentive to fix something that allows rich and / or inattentive customers to buy the same game 2-3 times.

Ah, I missed that one, so I made a new one. Ok I've upvoted that one too, thanks. This is partially implemented already on the home page via the "Additional content for your games" section, but it's short and only has 3 pages. It would imagine that it should be relatively easy for GOG to implement this into a proper filter.

That's incredible. It doesn't generate a gift code unless you specifically check that box, right? Why allow customers to pay multiple times for the same items?
As someone with a massive collection here, do you find that sensible? Do you just shrug off something like that, or does it make you feel like you've been swindled?
That section only shows me two things: items I've wishlisted and items I already own Edit: that the store doesn't mark as such. The only way to make it useful is a "Show all" button to see the full list.

That's right. No gift code, unless you tick the box, but that will obviously not resolve the lack of the ownership marker. I guess the idea here was to allow users to upgrade from a regular edition to deluxe, if there was no "upgrade DLC", however they will not give you a discount in such a case, whereas Steam would. So while you can upgrade by purchasing a whole edition, you will be completely negating your previous investment into the regular edition.

Do I find buying the same game multiple times just to mark it off as "owned" sensible? No, definitely not. Maybe if it was discounted to pennies or I liked the game so much that I desperately wanted to support the developer, I'd consider it, but generally no... nothing sensible about it. I did it once with BloodRayne bundles "for science", but that was about it. It was a waste, because the new bundle was just as broken as the previous one and I still don't have any of the individual games marked as owned lol (see attachment, the original "BloodRayne Complete Bundle" is no longer available, so it won't be shown here). I will definitely not be buying them a 3rd time, that's for sure.

Why don't I refund it? Because with GOG being so incompetent when it comes to user library safeguarding, I'm worried about how it would affect my library. Would it strip me of all the BloodRayne games, because I only get one copy of each, despite having purchased them twice, or would I maintain them from the previous bundle, despite the refund of the new bundle? Who knows with GOG... I'd rather just accept the sunken cost in this case and not open pandora's box of never-ending support tickets and elaborate explanations to support staff.

Well hopefully they'll implement more filters to the store, especially for DLCs.

The only relevant community wishlist entry I know of is Discount from bundles/GOTY etc if basegame/DLCs are already owned.
And now we'll never know if 3 purchases is exactly how many it takes to mark individual parts of a bundle as owned.
I'm sure if they yank the games from your account they'd issue you a gift code. But you do need to provide proof of all the purchases. From what I've seen in other threads about games disappearing from libraries, you can't simply ask GOG to search their own records. In fact, several people mentioned things disappearing from the Orders History page. Always good to have copies of those, and the e-mail receipts as well.

Hmmmm... I'm not saying there isn't a problem, but I checked my library and all of the games I own that you've listed above are still there, which means it's probably more of an issue with data corruption or API shenanigans than GOG's own malintent (at least not when it comes to actual games... bonus content however, yeah...).

Not that it makes the situation any better for those who are affected, but at least we know the GOGbears haven't gone evil... it's just the usual GOG jankiness, I'm "happy" to report.

Keep your backups up to date and replicated, people - that's what offline installers are for. Nevermind situations like the above, but GOG is a business and you may never know which way the ship is steered. We have a good idea now, but if ownership changes at some point, all bets are off. That's just the world of business, not something you should be particularly concerned about when it comes to GOG.

This!

We know that they've thankfully not gone evil yet, but we also know that their database is extremely poor and that their bundles very often cause problems. I do have my offline installer, but that doesn't mean we shouldn't report their usual mess ups. Some people may not have backed up their games either. As I stated in my original thread, the loss of Three kingdoms Story: Conussia is almost certainly the result of the expired promotional bundle. This is far from the only time that something has vanished once the promotion has ended, whether it be a bonus game or pre-order DLC, or whatever. They've still not replied to my thread or the ticket either.

I used to update my offline installers once every few months, but after they swapped my high quality Scorn artbook pdf for a low resolution and chopped-in-half ebook, and increased its price lol, I started downloading offline installers immediately after every purchase. I still have my HQ pdf, which I downloaded on the day of release, but everyone who did not bother downloading day one, may be oblivious to how they got scr3wed over. If GOG cared a little bit more, they would have left both versions for those who pre-ordered or bought on day one. This is like that Wolfenstein situation where Bethesda replaced a game with less bonus levels in it and caused an outrage. No outrage for an artbook of an obscure game though, so no fix either.