Using a unique branch per site is probably the wrong move since it really doesn't consolidate anything. All it does is move all the redundancy a bit further upstream. A better solution is to put more thought into your source tree's directory structure in order to support site-specific bits where needed. I gave a presentation about this very topic at PuppetConf a few months ago. Just search for Adam Kosmin PuppetConf and you should find it.
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