Hi Derek, I assume by "bad links" you mean pages on your domain that are returning a 404 error?
If this is the case then there're normally two things I do in these situations.
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Once I've found the list of 404s I'll look at the page authority of that page in open site explorer (the URL will still show results even if the content is no longer there).
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If any of these 404 pages are being linked to from EXTERNAL pages then I'll 301 those pages to the most similar other page on the domain.
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Run Xenu Link Sleuth (it's free, Google it if you don't have it) over the domain and find every link to these 404 pages.
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Manually go through and remove these dud links.
Hope that helps!
301 redirects should always be used if you delete a page that's built up links from external pages (or if you've merged the content into a larger page).
