But what are some good ways of "donating" to worthwhile causes as a small company or a freelancer? My accountant won't be happy if I just donate money directly without getting an invoice.

In the past I made a few "donations" by purchasing a "sponsored link" on project websites. Larger orgs, like the Apache Software Foundation, still accept corporate donations in this way, but the starting price is typically outside of my budget.

[1] https://news.ycombinator.com/item?id=44071321