The Boston Marathon gives exemptions to specific charities: http://www.bostonmarathon.org/BostonMarathon/Charity.asp

I believe they also give exemptions to runners who are local police, fire fighters, military, political dignitaries, etc. (but don't quote me on that).

I believe that many of the sponsoring companies receive blocks of enrollments for them to give to employees to represent the company in the run.  My brother runs marathons but is unable to qualify based on time.  He works for HP and tells me that they have an annual lottery/drawing for all runners who want to participate in the Boston Marathon (I believe they receive around 50 enrollments to give out).  He has been trying for several years and hopes to be drawn for next year's run.  There are no qualification times required but they do start at the back of the race.

Hope that helps,

Kevin