Pros
HHMI is one of the most successful research organizations in the country and employees are generally proud to contribute to the mission. Benefits (health care, sick leave, retirement) are outstanding, and offices are nice. On-site cafeteria and gym at HQ; field employees at universities enjoy comfortable, flexible research budgets and great prestige.
Cons
Executive management operates with a great degree of freedom and power, leaving on-the-ground employees confused by lack of a centralized strategy (or the ability to contribute to one). Logic behind different policies and programs is inconsistent because they are managed by different powerful people. Promotions are rare and raises (even for highest performance ratings) are usually 1-2%. Huge double-standard between the way working scientists are treated and valued vs. other professionals, whose contributions are undervalued. Layoffs/forced retirements are common and there is little effort made to retain oustanding employees.