The most conservative course is to try to stick to your budget and invest the excess money at the end of the year. This will give you something to draw on in emergencies, or money you can use in the future for something that the organisation really wants or needs to do.
"Invest" here doesn't necessarily mean putting money in the stock market, which usually doesn't make sense unless you have a lot of money, and you're willing to stay with it for a long period of time – ten years or more. Certificates of Deposit, which give high interest rates in return for keeping money in the bank for a set period (generally, you can choose a period of from six months to five years), or Money Market accounts, which give a high interest rate in return for keeping a large balance, are easy ways for an organisation to earn interest on its money, while still keeping it available for emergencies.
You can use your surplus to improve working conditions within the organisation: raise salaries, add a benefit package, etc. It is important to remember that once you've instituted this type of change, you're obligated to maintain it.