I just found this new HowTo at www.howtoforge.org:
http://www.howtoforge.org/secure_mysql_connection_ssh_tunnel
It describes how to set up a secure tunnel between your MySQL Server and a locally running MySQL Administrator using Putty. I haven't tried it out myself, but I strongly assume that this works for all the other GUI tools as well.
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Nice tutorial, but as far external tools are concerned I prefer Stunnel and I still think that a self contained solution is even better (MySQL does support secure encrypted connections without external tools and certificate based auth too).
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