I love trying to think of ways to make a startup do 'well and good', but donating to charity is a weak way of doing it. You're probably not making much money, so your donations will not have a substantial impact. Employees are more likely to feel that your $10,000 would have been much better utilized growing your company, than being sent to charity X to do who knows exactly what.

You can more directly do 'well and good' by doing well FROM doing good. Recently, I listened to a radio program about startups that were trying to do just that. For instance, one non-tech startup was based on collecting and selling unused fruits from people's yards. Employees can feel good because they have directly improved their community, by utilizing food that normally goes to waste.