The SEs treat the 301 as an announcement that they should disregard the URL which has the 301, and consider the redirect target URL as the permanent replacement URL for that content. In effect they treat old links to the orginal URL as if they were pointing to the new one (if all is done correct), because they treat as if the sites are linking to the content rather than the address. They see that the old links still point to the old URL, but they take it that the content those links voted for is now at new redirect URL, and generally do not give detrimental effect to the site that has used 301.

In practice I have always seen PR and link juice passed well by 301 and no bad effect on rank except sometimes temporary while SEs update.

Despite that, I would always try to get old important link from trustworthy and authority sites changed to point to new URL. No real reason other than I feel more comfortable that way. But no way would I spend time contacting 4,000 sites to ask them to change link!

In my personal experience (despite some people having a few problems) every 301 I have done, whether on Windows servers or Apache server all have worked very well with no issues beyond temporary blip.