I just stumbled across the MySQL GUI Tools Bundle which is very useful for managing a MySQL databases. In my opinion, it's much easier than using phpMyAdmin, which I had been doing previously. The only problem is that using it "requires" the machine the database is on (my web server) having an open external port (typically 3306) for the applications to have access to the database. "Requires" is in quotes because you can use PuTTY to open an SSH tunnel from your local machine to the database server, so that requests to port 3306 on your local machine are forwarded to the remote machine through the PuTTY connection.

Quick summary:

1. In PuTTY (before connecting to the server), go to Connections-> SSH-> Tunnels.
2. Add Source: "3306" (the local port you'll be using) and Destination: "127.0.0.1:3306" (the connection to be made from the other side of the tunnel.
3. Log into the server using PuTTY as you normally would. (Don't forget this step!)
4. Open MySQL Query Browser (or another of the tools), and for the connection info use Server: "localhost" and Port: "3306" (the local side of the tunnel), along with the appropriate username and password information.
5. The MySQL GUI tools should now work as normal. Enjoy.

For more information and screenshots, check out the link below.

[Source: realprogrammers.com]