Pros
The company does live by its mission statement and if you are an environmentalist and values driven person, you'll feel good about working for Patagonia. There is an opportunity for a good work-life-balance at Patagonia and the current CEO does seem to truly care about maintaining this, too.
Cons
The company has employees who don't leave and thus have very long tenure. While this means there is a great deal of historical knowledge, it can also mean that new ideas don't come in very often, or are simply not welcomed. This can lead to dysfunction in management and leadership. The relatively flat organization makes advancement difficult and the longer you work for the company, the more you can be underpaid; new hires often make more than existing staff in similar positions.