I'm writing my Bachelor's thesis in \LaTeX and I noticed e.g. Python and Matplotlib have a preferred reference they want you to cite to acknowledge the project as a whole. What is the best/most formal reference I should cite when I want to acknowledge the developers and the community as a whole?
Since it's a thesis and therefore an official document, if you want to say that your thesis was done in Latex (and so on), there's the colophon.
In publishing, a colophon is a brief statement containing information about the publication of a book such as the place of publication, the publisher, and the date of publication. A colophon may also be emblematic or pictorial in nature.
I'd use that. Actually I did use that in my own thesis, and — to be precise — I chose a rotated triangle shape. I still placed it at the end of my document though, after my bibliography.
There are many other shapes and you could choose no shape at all (just search images for "colophon"), but a simple paragraph seemed so bland to me, so I went for the triangle which still retains some sobriety.