Currently Wikipedia is doing a capital campaign in Germany asking for money. I wondered if I should donate via direct debit or paypal and wondered how much percent will Wikipedia (or other non profit organisations) receive from small donations (like 2€ / money for a cup of coffee).
It's a good question. We can't know for sure, but here are some things to think about.
Paypal advertises a discounted transaction rate for non-profit organizations. In the U.S. at least, the rate they advertise is 2.2% + 0.30 USD. There are lots of things that can come into play here, such as international rates or any special deal that Wikimedia has struck with Paypal, but it seems reasonable to guess that of your 2€ donation, Wikipedia sees perhaps 1.65€. Note that most of the fee is a flat rate; of the next 2€ in your donation, Wikipedia gets 1.96€.
Direct debit probably has lower fees. Paypal has to account for some credit card transaction fees in their fee structure, and direct debit does not. Therefore, I would guess that to maximize your gift, direct debit might result a little better than Paypal.
Charities, in general, don't want to tell you the best way to donate, because they want it to be as easy for you as possible, and don't want to discourage any type of donation at all. They are very happy to get any donation, even if one method over another results in slightly higher fees. Wikimedia, in particular, offers many different options for donating.
PayPal offers discounted transaction rates for 501(c)(3) charities for most products, and consistently low rates for all other nonprofits. No extra fees for setup, statements, withdrawals or cancellation. 2.2% + $0.30 per transaction and no monthly fee for charities.
There is a reduced rate if the donations total more than $100,000 (which they would for Wikipedia), but PayPal doesn't publish those rates. You have to call and ask about them. One forum I read indicates the rate drops to 1.9% + $0.30 per transaction.