Where and how do you keep your SSH and PGP keys?

KeePass and other

Yes anywhere. If only it was not clear that it's your keys and it's all keys.

Inside a truecrypt container) I may be overly paranoid

You speak as if we need a separate key for each service. If private piece of the recovery record is in the trusted store and zabekapit - just one or two, in production and test environment, for example.

In General, KeePass, as has been mentioned above.

ruToken, eToken, *token and other smart card or HSM.

what tools do you use to store SSH and PGP keys?

home directory. the question is exactly about linux?

There is no desire after reinstalling the system to create new keys and update them on servers or services such as GitHib

you can keep your home directory on a separate partition. and sometimes doing it backup.