SSH Tunnel support is available in Sequel Pro as of version 0.9.6.
Download Sequel Pro 0.9.6 (with Tunnel Support)
Download a copy of the latest version of Sequel Pro which includes support for SSH Tunnelling.
A tutorial on setting up an SSH Tunnel will be available shortly.
Note that 'Host' on the 'Standard' connection dialog is contextually different from the analogous 'MySQL Host' on the 'SSH' dialog. 'Host' in normal context is the fully qualified address of the MySQL server you intend to connect to relative to your current computer, for example a local 192.168.x.x IP address. The 'MySQL Host' field on the 'SSH' dialog is also the fully qualified address of the intended MySQL server you intend to connect to, but relative to the endpoint of the SSH connection you are creating. For example, if you are on a 192.168.2.x subnet and you SSH a tunnel to a 10.0.1.x subnet, the 'MySQL Host' field should contain a 10.0.1.x address.
Set up an SSH tunnel manually
Set up an SSH tunnel manually in Terminal using a command similar to:
ssh -NC matt@remotehost -L 9999:localhost:3306
Where ''remotehost'' is the host running the MySQL server (or is a host from which the desired MySQL logins are permitted). In the above example data/traffic on port 9999 on your computer will be forwarded to port 3306 (default MySQL server port) through an SSH tunnel, thus permitting you to connect to the remote MySQL server by connecting to port 9999 on your computer (localhost, with IP address 127.0.0.1).