It’s maybe not immediately obvious, but we have the facility to allow donations to apps included in the repository. Where we have the relevant information, which is a link, it’s included on the browse page for that app on the web site (e.g. http://f-droid.org/repository/browse/?fdid=org.mustard.android) and also via the menu in the f-droid client itself.
We don’t have as many of these links as we should, so if you know of any, or can find them, please post them in the corresponding thread here, or in the Submissions Completed forum.
Note that for it to make sense, it really needs to be a link to a specific donate page. If it just goes to a generic page with a donate button in a hidden corner, that isn’t going to make much sense in the context we use it. (In fact, for the example above, we asked Macno, the developer of Mustard, to create the page specifically).
One other thing to avoid – some apps have a paypal (or similar) donate button on their web site. Don’t use the link behind this button, unless the application’s developer has explicitly agreed and knows we’re doing it – the reason being that the might change it (e.g. to a different account) and we wouldn’t know, and they wouldn’t know we needed to know.