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I don't think going over the limit will actually damage your Mini. At least, I've never seen a machine get damaged from too much RAM. The RAM limit is basically a function of the logic board's chipset. The chipset just won't recognize anything above 2GB in the 2006 Minis. The 2007 (Core 2 Duos) are a bit of a different story. Apple claims 2GB is the limit, though Macsales.com and other sites and proven that you can install 4GB (Dual Channel, match pairs will give best performance), and the machine will recognize 3GB. The Core Solo/Core Duo models are stuck at 2GB, though.
 
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