If you're on a remote server with bash-ftw installed, and you're forwarding your local agent via either ssh -A username@host or the SSH config value ForwardAgent yes, and ssh-add -l shows The agent has no identities., this could be due to bash-ftw not detecting your forwarded agent from a previous session, and starting a separate SSH agent.
To fix this, check your home directory for a file like .ssh-vars.YOURHOSTNAME.sh by doing ls -a ~ | grep .ssh-vars, and remove any such matching files. Then, disconnect from your remote server and relogin via ssh -A.