Our database servers are not in house, but located at a hosting provider. We can only access them using SSH tunnels. So I start a tunnel on my machine:
ssh -N -f -L 3307:127.0.0.1:3306 user@1.2.3.4
where 1.2.3.4 is the ip to the hosted server. After that, I connect to 127.0.0.1, port 3307, e.g.
mysql -h 127.0.0.1 -P 3307 -uuser -p
This works, but is inconvenient. Maybe you could add ssh tunneling into Jet Profiler, so I wouldn't have to set up the tunnel everytime I want to connect?
How is the development of this idea going? It seems not to be implemented yet, almost 2 years later. For an idea of what it could look like, have check out HeidiSQL.