We use StartCom to issue a lot of certificates for sensitive internal hostnames. While we don't rely on security by obscurity, we'd really prefer it if our internal hostnames weren't published all over the internet... :\
Given Lets Encrypt does this too, I'm not sure what other options we have with regards to certificates without paying on a per-certificate basis. :( I like StartCom's model of only paying for verifications (i.e. the only thing which really directly costs money).
We definitely want our EV certs going to CT logs, but not any of our wildcard or Class 2/3 certificates.