Is there a citation manager which plays nicely with BibTeX and has automatic metadata import from PDFs?

JabRef also supports metadata extraction and works on Linux, Mac, and Windows (and maybe others).

Give BibDesk another chance.

It's highly integrated with Google Scholar and other search engines. In case you need to keep the .pdf-files in your local library, just drag them onto the publication and BibDesk automatically files them for you.

Apart from the full-text-search right from BibDesk I really like the integration with the pdf-reader Skim. All the highlighted text and annotations can be viewed directly from within BibDesk. Plus, you can search through them.

You can even view your Skim-notes direclty in BibDesk's preview-pane, if you use this BibDesk-template: http://ug.bu.edu/blog/lingtech/2009/03/22/even-better-bibdesk-preview-pane

TL;DR: I heart BibDesk.

I need to answer this question myself because I am stupid.

BibDesk supports all the features I wanted. It simply never occurred to me to try this out, I’d simply always manually imported references instead of just trying to drag a PDF onto it. I feel like deleting the question but perhaps somebody else finds this useful after all.