citizenlab.ca/2022/09/statement-on-the-fatal-flaws-found-in-a-defunct-cia-covert-communications-system/ did an investigation and found 885 such websites, but decided not to disclose the list or methods:
Using only a single website, as well as publicly available material such as historical internet scanning results and the Internet Archive's Wayback Machine, we identified a network of 885 websites and have high confidence that the United States (US) Central Intelligence Agency (CIA) used these sites for covert communication.
The websites included similar Java, JavaScript, Adobe Flash, and CGI artifacts that implemented or apparently loaded covert communications apps. In addition, blocks of sequential IP addresses registered to apparently fictitious US companies were used to host some of the websites. All of these flaws would have facilitated discovery by hostile parties.
The websites, which purported to be news, weather, sports, healthcare, and other legitimate websites, appeared to be localized to at least 29 languages and geared towards at least 36 countries.
The question is which website. E.g. at citizenlab.ca/2021/07/hooking-candiru-another-mercenary-spyware-vendor-comes-into-focus/ they used data from Censys.
We searched historical data from Censys
citizenlab.ca/2016/08/million-dollar-dissident-iphone-zero-day-nso-group-uae/ mentions scans.io/. citizenlab.ca/2020/12/running-in-circles-uncovering-the-clients-of-cyberespionage-firm-circles/ mentions: www.shodan.io/, Censys really seems to be their thing.
Another critical excerpt is:
The bulk of the websites that we discovered were active at various periods between 2004 and 2013. We do not believe that the CIA has recently used this communications infrastructure. Nevertheless, a subset of the websites are linked to individuals who may be former and possibly still active intelligence community employees or assets:
  • Several are currently abroad
  • Another left mainland China in the time frame of the Chinese crackdown
  • Another was subsequently employed by the US State Department
  • Another now works at a foreign intelligence contractor
Given that we cannot rule out ongoing risks to CIA employees or assets, we are not publishing full technical details regarding our process of mapping out the network at this time. As a first step, we intend to conduct a limited disclosure to US Government oversight bodies.
This basically implies that they must have found some communication layer level identifier, e.g. IP registration, domain name registration, or certificate because it is impossible to believe that real agent names would have been present on the website content itself!
The websites were used from at least as early as August 2008, as per Gholamreza Hosseini's account, and the system was only shutdown in 2013 apparently. citizenlab.ca/2022/09/statement-on-the-fatal-flaws-found-in-a-defunct-cia-covert-communications-system/ however claims that they were used since as early as 2004.
Notably, so as to be less suspicious the websites are often in the language of the country for which they were intended, so we can often guess which country they were intended for!