Pros
Amazing paid time off; inexpensive, rich health benefits (for individuals - family coverage can get pricey); many caring, mission-driven employees; one of the larger organizations in the area by headcount; free covered parking; casual work environment; Agency supports some terrific and diverse local social programs; organization is funded through fairly stable sources; relatively flat organization means you can run with projects and your ideas are listened to.
Recently leadership has invested in and revamped the support functions - IT, Accounting, HR. Changes are already evident and are hopefully the start of big things to come for the Agency.
Cons
Working for a non-profit can be challenging, as resources aren't always as plentiful as in the for-profit realm. You can be relied upon to wear many different hats to get the job done, and this can be a positive or negative depending on your attitude.