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It's free for the community edition, which is all you need if you don't need HTTP tunneling (if you're on a shared host, you won't be able to use it on your remote server without it; if you have a static IP at the client end and you control permissions on the ports and such on the server end, I think you can use it remotely, but you still may need the enterprise edition).
I suspect in any case that the paid version is cheaper than the SQL Server 2005 Management Studio, but I don't recall.
PHPMyAdmin of course has the virtue of being free and working in almost all situations, but I find it quite cumbersome. That's not a criticism of PhpMyAdmin's design or anything, but just noting an unavoidable downside to a browser-based client.
So I usually use SQLYog locally on my sandbox projects and then just use the default MySQL command line client from the shell on the server.