Here is my experience in using software to organise scientific publications. I use for a few months. Previously I used Mendeley Paperpile and Google Spreadsheet . They have nice functionality but also some nuances. Justin mentioned the Endnote but I did not like at all. Guys above already mentioned these. Zotero is nice but I prefer reusing knowledge that was extracted by others. BibDesk became recently unusable. Although it is an open source so you can improve it yourself. PDFs are too annoying. I had piles of them on my hard drive. Tree-like structuring of files is not good. I like the graph-like or mindmap-like distribution of cross-s. From last summer I use BioMindmap to organise scientific proofs for the topics I am interested as a researcher. (I am not a lab researcher but a -researcher I would say.) Pros Free software. Citations are color-coded Scorecard that shows the validity of proofs Automatically fetches publication meta author year etc When you submitted enough you are approved to add more without premoderation queue. As it is collaborated tool someone can change your entries (as in wikipedia) if the user is reputable. Maybe this is not expected. Mostly PubMed is considered a good source. But there are about 1 other domains that are ok too. Check FAQ on the website. ordered-list