I'm afraid that question is a bit too open ended to get a good response. We'd have to know a lot more about your current position and the new company to give you anything of value. Also we'd have to know a lot more about your current job responsibilities and those required by the new firm.
Ex. A non-profit might require you to use open source tools while a specific company may require proprietary tools. It all depends on the companies.
From an employee's perspective, there's no overall difference that you can attribute to the tax status of the organization. There is tons of variety in "corporate style", just like there is in NPO sector.
NPO's can be uptight or utracasual, with or without dogma, overflowing with money or operating on a shoestring, embracing open source or shunning it, offering hypercompetitive salaries or undercutting the average.