What does your BibDesk look like?
Show us how you're using BibDesk. What search groups are you using? How do you organize your publications table? Let's see.
I have been using BibDesk for a long time, so I built up some pretty old habits. I have all my references in one file (463 pubs right now) and I tend to treat it like GMail - I don't organize it with groups, I use the search field to find what I want. I make heavy use of keywords, and usually I have the groups pane displaying keywords, but I still tend to use search to find the keyword I'm looking for. I also don't use smart groups (old habits!)
I usually find PDFs online through people's personal sites or either the ACM/IEEE libraries or Google Scholar. Most of the time, there is BibTeX on the site I can copy and paste into BibDesk, but the rest of the time I use the "New Publications from Web" feature in BibDesk, my personal favorite recent feature.
My favorite early feature is the transparent character translation from TeX entities into regular characters for display. It's easy to take for granted, but I think this is what makes BibDesk feel like a real Mac app more than anything else. It always sticks out when I see other bib apps.
Of course, my favorite feature of all-time is AutoFile. If you're not using AutoFile, you're not really using BibDesk.
(No screenshot forthcoming)
I've been using BibDesk since before Mike hosted it on SourceForge, and at that time mainly used it as a way of manipulating a BibTeX file without worrying about BibTeX's arcane syntax (or lack of syntax). One of my favorite features when writing my dissertation was the citation autocomplete, using our input manager hack; since my database had grown to >400 references at that point, I could no longer remember cite keys, and entering a citekey in iTeXMac based on title/author/keyword was really cool.
Since that time, I've mainly used BibDesk to store and search literature (using AutoFile for organization, of course!). Some of the online databases I use frequently have RIS export, so I tend to add articles as RIS when possible. I have a few smart groups, oriented towards specific projects I'm working on, but I also rely mainly on keywords for organization.
One of my favorite features is the File Content search (I'm biased, since I wrote it), but I use it fairly regularly to search the files associated with my references. The main differences between this and Spotlight are that the search is focused on the files currently attached to the references, and it searches text content instead of metadata. It also doesn't freeze like the Finder, or lose your selection like the Spotlight window!
As far as cool hackery, I think the macro capability is one of the best features we have; I'm not aware of any other BibTeX application that displays the expanded macros and allows you to edit them easily, or handles crossrefs. That was a major addition to the program.
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