jamyskis: So, after some digging, I've found out what's going on. It seems the BPjM have turned their vile eye to digital distribution storefronts, which fall under category of broadcast media. Games and movies that are illegal to distribute openly are placed on Lists C and D (the analogues of the physical media lists A and B, so C is the general risk to children and D is breaking the law).
So:
Aliens versus Predator Classic
Blake Stone: Aliens of Gold
Blood: One Unit Whole Blood
Blood II: The Chosen + Expansion
BloodRayne
BloodRayne 2
Carmageddon Max Pack
Carmageddon 2: Carpocalypse Now
Harvester
Kingpin — Life of Crime
NAM
Painkiller Hell & Damnation
Painkiller Overdose
Postal 2
Postal 3
Rise of the Triad: Dark War
Rune Classic
Shadow Warrior Classic Redux
Star Wars: Dark Forces
The Chaos Engine
TimeShift
UberSoldier II
jamyskis: Have likely all gone into List C
Painkiller: Black Edition
Postal
jamyskis: Have likely gone into List D
POSTAL Redux
jamyskis: Is a new addition and has probably gone into List D.
Rise of the Triad (2013)
jamyskis: Is a new addition and has probably gone into List C (may also be a mistake, as the 1995 game was indexed twice - once under the name Rise of the Triad: Dark War, once under Rise of the Triad).
SiN Episodes: Emergence
jamyskis: This is probably on List C, but is very likely to be a mistake, as the version distributed over Steam was the USK-cleared censored version.
Everything else that was indexed on Lists A and B and was already not available on the Steam Store at the behest of the publishers has probably now been made official on Lists C and D.
Duke Nukem 3D: Megaton Edition is probably there as well would have been removed if it hadn't already been pulled for licensing reasons.
The indexed uncensored version of Far Cry is apparently still up.
Expect GOG to follow suit in the near future.
You know that the BPJM can't do anything when it comes to websites and companies which are not placed in Germany? They can index that specific site but that is all they can do. If a site is indexed it does not show up in German search engines like google.de (google.de, bling.de and so on are using the BPjM filter) if you use google.com (what is suggested anyway) it does show up because the BPjM filter is not active. That is all they can do, they can't block sites and they can't force stores to remove games for German customers.
The last shop they wanted to index was Gameware which never happend and if you have seen the BPjM filter leak there are a few shops on that list but all of them sell Nazi stuff the rest is porn and some weird stuff like a gameserver site from a gaming clan (with .de adress).
The best example for this was the reddit case when reddit blocked a website for German users and argued that the BPjM forced them to do this. People smelled censorship and magazines like Spiegel, Focus and so on brought news about it. The BPjM released a official statement that they never asked that this specific site has to be blocked (they don't have the right to do this which are their own words) and that the only thing they could do is indexing that site which would lead into the restrictions above (not visible on German search engines) nothing else.
The problem is that Publishers are overreacting and blocking games which makes no sense at all because adults are free to buy them anyway. Square Enix as example completely blocked Sleeping Dogs: Definitive Edition for PC so you can't activate, install or play the game with a German IP. You can buy this game in any store which sells indexed games in Germany but only for console because of the reasons above.
Also people always think that the BPjM would index Wolfenstein and Co. because of the use of Nazi symbols but the truth is that the criminal code 86a (use of forbidden symbols) is not mentioned as a reason for the index in the youth protection law. The BPjM can't index games because of Nazi symbols. Hope this myth is busted now!
*BPjM called Bundesprüfstelle für jugendgefährdende Medien in english Federal Review Board for Media Harmful to Minors.