There are a few options to accomplish this:
1. You could use a standard paypal donate button and embed it with plain HTML.
2. Another idea would be to create a product called "Donation" with a default price of $1.00. Then the website visitor could adjust the quantity to adjust the price. So a quantity of 5 would result in a $5 charge. Doing it this way, you could use Cayan and I believe they offer better rates and fees for non-profits.
3. I have also noticed that many donation based sites use standard amounts. So they may have a $10 donation, $25 donation, and $50 donation. I think they do this to make donating not require a consideration of, "How much should I spend? What is everyone else donating?"