The top five, with their scores:

Donnie Darko: Director's Cut     71.2
The Corporation                  36.8
Napoleon Dynamite                28.7
De-Lovely                        19.6
Control Room                     18.0


I've come up with a way to identify the movies that have great "word of mouth", which is different than great total box office.  The movie has to have been out for at least 3 weeks, and you get the score by multiplying the number of weeks out by the dollars per screen (in K dollars).   In other words, still filling the theaters after being out for awhile, which is usually due to great word-of-mouth.  

This tends to identify "small" films which friends are recommending to friends, but blockbusters can make it onto the list too.  

I'll try to put this list up every week, based on on current info from rottentomatoes.com, my favorite movie review site.