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Comment of G.Zanferrari:
I was no allowed to connect with SqlYog to mysql installed on another server. The problem was that the default root user created at installation the 'localhost' permissions has.
Thus: root@localhost

I changed it to:

root@%

and the problem was solved.
Added at: 2007-03-29 10:01

Comment of Hammad:
On windows, you need to turn off windows firewall or let traffic on your mysql server port through on both sides - the client and server machine.
Added at: 2011-10-17 04:43

Comment of Andrew:
If you're trying to connect to a SQL Server hosted by a host such as iPage, you need to connect using HTTP Tunneler because the port is blocked. This is easy, simply upload the SQLyogTunnel.php file from the SQLyog root directory to the root directory of your server then use the HTTP tab when making a new connection.
Added at: 2013-10-11 05:15