I would assume no one has mentioned Tinderbox because (a) it's $250, and (b) is Mac only. I'm just guessing that this has served to self-filter a lot of folks here (Linux/Windows/open-source-only folks have no idea of it).

Calibre is a multi-platform alternative to Bibdesk, the UI is ugly but it's very usable.

I am sorry but Calibre and Bibdesk are completely different programs. I have used both programs and I am surprised you would say that calibre is an alternative to bibdesk. Calibre's focus is ebooks and bibdesk's focus is bibliographic information. The only possible overlap is that they both create a directory with electronic reading material. In order to get calibre to organize a directory like bibdesk (ie configured by author/journal/year) you have to jump through a million hoops and it requires duplicating your library. Have you ever used Bibdesk?

I grudgingly use calibre for epub/mobi conversion. Calibre's UI is ugly and it is not very usable: there are three separate pairs of arrows on the ebook preview screen! How would you decide which pair is for pgup/pgdn? And what would a user expect the use is for other two sets?