My colleague Andrew Westgarth has just sent me a link to the following blog post that shows you how to deploy webpart solutions without having to mess about with individual web.config files. Takes a little bit of time to setup but worth it in the long run!
http://leedale.wordpress.com/2007/05/31/deploying-a-webpart-solution-in-sharepoint-2007-the-simple-way/
Alternatively Andrew Connell suggests this way to create your WSP file
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