I just put together a plugin that will allow you to add StatCounter's code to your WP site quite easily. See here for details.
Credits where credits due, this was heavily inspired by Matt Labrum's Google Analytics plugin.
I installed this plugin under WordPress 2.0, activated it, added my statcounter project code in the options screen, saved options and when I checked the source of my pages there was no statcounter code in any of them.
In short - it doesn't work for me.
That makes me sad :(
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