Assume you have a CER is an DER encoded X.509 certificate in binary form, and you want to have a PEM-encoded X.509 Certificate file for Apache.
The following command may help:
openssl x509 -inform DER -in certfile.cer -out certfile.crt
Apache/mod_ssl request PEM-encoded X.509 Certificate file
Description: Server PEM-encoded X.509 Certificate file
Syntax: SSLCertificateFile filename
Context: server config, virtual host
Override: Not applicable
Compatibility: mod_ssl 2.0
This directive points to the PEM-encoded Certificate file for the server and optionally also to the corresponding RSA or DSA Private Key file for it (contained in the same file). If the contained Private Key is encrypted the Pass Phrase dialog is forced at startup time. This directive can be used up to two times (referencing different filenames) when both a RSA and a DSA based server certificate is used in parallel.