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Can I ask what do you mean by "questionable" links...I can't imagine anyone doing white hat seo would have anything that would be questionable? Can you describe these links please in terms of the type of site that they were on and any significance in anchor text and also how long did it take you to remove them?

I totally agree Matt.  When we take a step back and ask "do these pages look like they're written for a search engine", that allows us to start to see the unnatural patterns that come from that type of approach that's geared toward ranking and not users. I also put a lot of emphasis on that concept though - unnatural patterns.  Think about the greater web outside the small world of SEO driven sites.  Is it natural for someone who has NO clue about SEO, to repetitively use the same keywords over and over in link anchor text? Absolutely not. Apply that same rule to every other aspect of the work. Do NOT however, throw out the principles of Information Retrieval in the process.  Proper page titles, proper (and appropriate use) of keyword specific anchor text, H1s, H2s, breadcrumbs, content and topical organization -these are all CRITICAL to Information Retrieval, going back to the days of library index card systems (adapted to web content).  And that's true even without SEO.

Exactly my point. This is why I dont see it being a ranking factor and if it is... they will have to manually determine good from evil.

Thanks @Nakul for your useful input to this question.  Yes, agreed.