If a computer and/or key is compromised, well, I just nuke all the related keys.
I don't understand the desire to manage a large number of keys since the attack surface is pretty clear:
A) The machine is not compromised and the key is safe.
B) The machine is compromised and the key should be replaced ASAP.
C) As a byproduct this forces obsolescence of keys in the ~3-4 year timeframe and you really should be swapping out keys every so often anyway. This keeps you from ignoring this fact for a decade :p
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I use ssh-agent and 1 key per computer.
If a computer and/or key is compromised, well, I just nuke all the related keys.
I don't understand the desire to manage a large number of keys since the attack surface is pretty clear:
A) The machine is not compromised and the key is safe.
B) The machine is compromised and the key should be replaced ASAP.
C) As a byproduct this forces obsolescence of keys in the ~3-4 year timeframe and you really should be swapping out keys every so often anyway. This keeps you from ignoring this fact for a decade :p
Similar, with forced key rotation. Remote key files are managed with a home brew script for assembling and distribution of authorized_keys