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bunltd - 6:45 pm on Apr 24, 2012 (gmt 0)
Well, best practices wouldn't edit the core WordPress files at all but make any changes via the theme's functions file or plugins.
Doing it via the theme's functions file or a plugin means you spend the time once and can update WordPress core with no issues - doing it in the core WordPress files means you spend time everytime WordPress updates to make your changes again.