The Heritage Foundation and FreedomWorks are the two main "think tanks" associated with protesting healthcare reform. The differences between them are as follows:
Heritage Foundation is much larger and ingrained in US Government and Media than FreedomWorks. They specialize in media manipulation and dissemination of propaganda but they also help to organize protests and faux townhall-style activism.
FreedomWorks has more control over the actual protesters and activists than Heritage Foundation does because they specialize in rallies, robo-calls and ground-level training.
Read more on the Heritage Foundation here and here and especially here.
Another anti-healthcare reform advocacy group that works closely with the Heritage Foundation and in much the same manner is FreedomWorks which you can read about here and here.