From TFA, the CAs that use MD5 are these:
* RapidSSL
C=US, O=Equifax Secure Inc., CN=Equifax Secure Global eBusiness CA-1
* FreeSSL (free trial certificates offered by RapidSSL)
C=US, ST=UT, L=Salt Lake City, O=The USERTRUST Network, OU=http://www.usertrust.com, CN=UTN-USERFirst-Network Applications
* TC TrustCenter AG
C=DE, ST=Hamburg, L=Hamburg, O=TC TrustCenter for Security in Data Networks GmbH, OU=TC TrustCenter Class 3 CA/emailAddress=certificate@trustcenter.de
* RSA Data Security
C=US, O=RSA Data Security, Inc., OU=Secure Server Certification Authority
* Thawte
C=ZA, ST=Western Cape, L=Cape Town, O=Thawte Consulting cc, OU=Certification Services Division, CN=Thawte Premium Server CA/emailAddress=premium-server@thawte.com
* verisign.co.jp
O=VeriSign Trust Network, OU=VeriSign, Inc., OU=VeriSign International Server CA - Class 3, OU=www.verisign.com/CPS Incorp.by Ref. LIABILITY LTD.(c)97 VeriSign