PEM on it's own isn't a certificate, it's just a way of encoding data. X.509 certificates are one type of data that is commonly encoded using PEM.
PEM is a X.509 certificate (whose structure is defined using ASN.1), encoded using the ASN.1 DER (distinguished encoding rules), then run through Base64 encoding and stuck between plain-text anchor lines (BEGIN CERTIFICATE and END CERTIFICATE).
You can represent the same data using the PKCS#7 or PKCS#12 representations, and the openssl command line utility can be used to do this.
The obvious benefits of PEM is that it's safe to paste into the body of an email message because it has anchor lines and is 7-bit clean.
RFC1422 has more details about the PEM standard as it related to keys and certificates.