This is a good question, and the answer is one that everyone in guild has the right to know (after all, it is your gold). The guild fund is used for a variety of things:
1. Helps balance out salaries. We only get the Naotun tax every Kingdom War week, which is much higher than non-Kingdom War weeks. If I didn't maintain a guild fund, then one week you would get between 5M and 10M. Also, I wouldn't be able to pay any bonuses (Kephra).
2. Helps to pay out kephra killer bonus.
3. Helps to cover some items that would be used for guild wars. Some great pots, naiads, horse feed. However, you should be collecting these things in the event of guild war. The guild would not be able to supply 100+ people with everything needed, just help some people who can't get their hands on needed supplies quickly.
Currently I'm keeping approximately 2B in the guild fund, which should be higher (3-4B is a much more comfortable cushion in the event of guild war).