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Rather than request a public key to put into the user's authorized_keys, I would rather generate a key I can send to the user and tell them to use with their client,

ssh -i keyfile.pem host.server.com

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you typically would just generate the RSA/DSA keys for the use with ssh in this manner. If you are generating a x.509 certificate including the private key, x.509 would not have any significant advantage over the much simpler RSA/DSA authentication. –  the-wabbit May 16 '11 at 16:29
    
Can you guarantee that you can send the private key and it's pass phrase to the user in a safe manner? –  Iain May 16 '11 at 17:36
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You're still looking at generating a keypair (with a tool like ssh-keygen) and sending the user the private key in order to connect to your server. Note that this creates a few security problems. Namely you need a secure way to get the private key to them, and they lose the ability to control their private key.

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