Censys

 https://censys.io/

Censys performs regular scans for common protocols (e.g., DNS, HTTP(S), SSH). Provides a search for TLS certificates.

Access is free, but requires registration. The website no longer provides free bulk access. Bulk access requires a commercial or a research license. The free access is limited to 1000 API calls per day.

@InProceedings{censys15,
    author = {Zakir Durumeric and David Adrian and Ariana Mirian and Michael Bailey and J. Alex Halderman},
    title = {A Search Engine Backed by {I}nternet-Wide Scanning},
    booktitle = {Proceedings of the 22nd {ACM} Conference on Computer and Communications Security},
    month = oct,
    year = 2015
}

Certificate Search crt.sh

 https://crt.sh/

Certificate search engine. crt.sh is based on the certificate transparency logs and provide wildcard search for domains.

Common CA Database

 https://www.ccadb.org/

The Common CA Database provides links about general information about CAs and information about their root stores. This covers the root stores of Mozilla, Microsoft, and Google Chrome. Many other useful links are also available, for example, certificate searches and explorers.

Google Transparency Report

 https://transparencyreport.google.com/

Google's Transparency Report contains various information. It provides information about email encryption, HTTPS encryption, information about potentially harmful applications in Android, and live reports of traffic disruptions, such as censorship.

It provides a certificate search based on the certificate transparency logs, similar to crt.sh: https://transparencyreport.google.com/https/certificates

Mozilla Observatory

 https://observatory.mozilla.org/

Website quality measurement tool. The website measures the quality of HTTP headers which improve security. Additionally, it provides inspections for the TLS certificate and SSH servers. It also includes many third party tools.

Passive SSL (CIRCL)

 https://www.circl.lu/services/passive-ssl/

Historical certificate dataset. Allows querying based on IP address or certificate.

Qualys SSL Labs

 https://www.ssllabs.com/

Test the quality of a server's or a client's SSL/TLS stack. Very useful to test a server. Provides a A-F rating scheme and shows vulnerabilities and weak protocols/cipher suites.

RIPE Atlas

 https://atlas.ripe.net/

RIPE operates a set of probes, which can be used to send pings or similar measurements. The probes are mainly placed in Europe but some are also in other continents.

All the collected measurements can be found in the RIPE Atlas Daily Archives. The blog post gives some more details.

RsaCtfTool

 https://github.com/RsaCtfTool/RsaCtfTool

The RsaCtfTool is a tool supporting working with RSA keys. The main focus lies in a wide range of known attacks which are implemented and easy to use with it. This makes it suitable for CTFs, especially Jeopardies.

Shodan

 https://www.shodan.io/

Shodan performs regular scan on common ports.

Access is free, but requires registration. More results can be gained with a paid account.

badssl

 https://badssl.com/

Test the quality of a client's SSL/TLS stack. The website shows sites which should fail or pass. Sites which fail but do not on the browser viewing are a risiko.