Connecting to a remote machine with a public key using Fugu
Note: I found entering -i ~/PATH/TO/ec2-keypair.pem didn't work for me, but another workaround in the same field worked.
In the &quot;Advanced SFTP Options&quot;, in the same Additional SSH Options dialogue enter:

-oIdentityFile=~/PATH/TO/ec2-keypair.pem

So, for example, if your EC2 instance looks like

root@ec2-123-45-678-910.compute-1.amazonaws.com

with your key being at the root and named

ec2-keypair.pem

then the relevant input is:

Connect to: ec2-123-45-678-910.compute-1.amazonaws.com
Username: root
Additional SSH options: -oIdentityFile=~/ec2-keypair.pem

Hope it works for you!