A friend of mine, who wrote his thesis (of about 1, 40,000 words), suggested this to me. I've been using the Windows version for over 2 years, and found little reasons to complain. I store around 6000 citations, along with annotations and links wherever possible to pdfs on my machine. The manual input method is actually a boon: it helps you identify and correct errors unlike automated fetches from Google Scholar and other sources when using software like Zotero, Mendeley, and EndNote. Also Zotero crashes often; Mendeley pretends to be free (asking you to upgrade after a point), and EndNote is... well, it sucks. JabRef is consistent, the easiest to understand, and the most reliable bibliography citation manager. Much thanks to the developers!
I have over 2500 references in my bibliography and JabRef handles them with ease. This is one of the most useful softwares I have used when writing papers.
I tried many, this beats all. Very consistent. Lives well with your hand-generated bib files as well.
Unfortunately you need to enter most data by hand. This gives good control on small bibliographys but is tedious if you have many references. In the second case I prefer Mendeley Desktop available as *.deb package as well.
Comfortable tool to keep all the papers ordered. It has a online search for article, but many journals are not supported.