Why do pages with a 404 error drop out of webmaster tools only to reappear again?

[Towelsrus]

I have noticed a lot of pages which have fallen out of webmaster tools crawl error log that had bee 404'ing are reappearing again

Any suggestions as to why this might be the case? How can I make sure they don't reappear again?

[Host1]

Based on my experience it's usually some incoming links/links that you have missed that causes this.

A 301-redirect to a working page should fix this permanently.

[Towelsrus]

I think you are right here, however the pages have links from sites we now probably don;t want from a  link build perspective. I am concerned that these links (mainly low PR sites, forums etc) may do more harm than good so to funnel any link juice they have may be more damaging.

Any other suggestions here?