Pros
The benefits are very good. Employees usually have more paid time off than their peers at competing employers. The retirement plan seems to be better than most companies, but comparable to competing academic institutions. Shifting hours to be a bit off from 9-5 seems to be easy and common. Employees have access to great equipment to complete their projects. Opportunities for training or taking a class are good. Internal seminars and invited speakers are good. Employees tend to be some of the brightest people around.
Cons
Managers come from purely technical backgrounds and do not appear to receive much management or leadership training. They may be good at winning grants, but they can be quite bad at handling necessary administrative or personnel issues. Ironically, the tuition reimbursement for continuing education is worse than at competing employers and academic institutions. Salary does not seem to be competitive with industry. Women and minorities are very underrepresented in management.