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What kind of links are they? Do they contain spammy, non-related anchor text? If they are simply old links that don't exist any more or are from sites that have been devalued you should not worry too much about removing them. Google simply devalues the link juice running through them to your site. It is true many sites have been devalued from Penguin, but it simply means that these sites don't pass any value onto your site - while they also do not harm your site unless they are of a bad or negative nature.