- Is it better to use a different passphrase on each key, or does using the same one not matter much?
Yep in an ideal world, though I suspect in practice it doesn't matter much.
- How much less secure is it to not use a passphrase on a key?
You are relying completely on the security of your disk, against either physical or cyber. Use a passphrase, use an agent to manage it.
- Should you use a different key per user account, per server, or per use-case (i.e. personal or work)?
Per client device. This is the device that can be compromised and cause invalidation to be required, so this is the one which should be seperate. For convenience you can maintain all your devices public keys concatenated together and hand them out like that - comment each with hostname and date created for ease of identification.
- Does increasing the amount of bits in a key really have an effect on the security of the key, or does it not make much difference in a real-world use?
Up to a point. RSA in 8 bits is trivial. Go for a highish key length, different key types have different recommended lengths. Note some machines dont support higher lengths.
- How/Where should private keys be stored on a device using them?
In $home/.ssh
Permissions should be set for only you to read with no writing. Even better if your home drive is encrypted as it is only vulnerable whilst you are logged in.
- What are some of the pros and cons from a security standpoint, and how may doing different things affect the usability of a key?
If you hop machines a lot key per client can be problematic. In this case a portable secure drive is useful. Of course one leak can be fatal here.
Try not to fall back on passwords, they have nothing like the same security.
Most usability issues are caused by the people running the servers not reacting in a timely fashion to key updates.