Running "ssh-keygen -t dsa" generates two files, a private and public key. Its simple enough to comprehend that the private key is used to identify yourself to the outside world, which only sees your public key.
However, I've also seen ".pem" files used as well, and I use them myself. Whats the relationship between the .pem file and pub files. I was hoping for a simple answer, but other questions (http://serverfault.com/questions/9708/what-is-a-pem-file-and-how-does-it-differ-from-other-openssl-generated-key-file) seem to indicate that there is no simple explanation for why a pem file might be better/worse in different scenarios to a pub file.