I'll speak up for bibtex files, while I was writing my doctorate I was adverse to spending time choosing between the different apps, so I kept an extra window with my master bibtex file (all the papers I read) open. This forced a beneficial habit of really critically reading and labeling to summarize each citation - 'This is why I find this paper important'. It probably would've been quicker to just throw em all in a citation manager, but I got great feedback in a "you really know your area, well-cited work" way when defending.