Software (for academics using Macs)
    If you're an academic scientist and Windows user thinking of switching to a Mac, I suggest you reconsider.  There are many software programs required by biologists that don't work on Macs including many statistical programs.  Even R is not as good on a Mac and can cause considerable frustration.  However, if you insist on switching, as I did, here is some helpful advice and useful applications.  First, hold of on buying Windows and running it on your Mac.  This sucks up a ton of RAM which is a problem if you are using it to run CPU-intensive programs (such as R, SAS, Photoshop, etc.).  Start with Wine Bottler and try running Windows programs through that on your Mac. It's free and uses much less of your RAM.  I have had mixed success with this and did end up running Windows XP through VMWare Fusion to run WinBUGS.  Also, don't buy the Mac version of MS Office if you don't have to.  It's different than the Windows version and doesn't include MS Access for data management.

Organizing and Managing PDFs and References
Organization and administration is an ever increasing part of any academic's or researcher's life. It begins as a small piece as an undergraduate and initial master's student but grows almost exponentially over time. Luckily there are numerous programs to help manage the academic's electronic life. Below is a list of programs and some useful links. Here is a link to one rather negative review of a variety of programs. You can find another summary of programs here. Also see these recommendations and this link for a nice comparison of the programs.

Papers - organize your .pdf files like iTunes does for music (mac only). Here is a video showing how to integrate Papers and Endnote.  I love this program but have not figured out a smooth workflow (or combination of existing files) for Papers-to-Endnote.

Mendeley - A great reference manager that I recommend for people who aren't Mac uses and therefore can't use Papers. It is better at linking to PDFs than Endnote.

Zotero - another excellent reference manager. I have less experience with this than the others but it seems very nice.

Endnote - citation manager that has been the standard for academics. Excellent for citations and you can link to the PDFs but it's not great for managing your PDFs like Papers or even Mendeley.

Bibdesk (Mac only, oriented for LaTeX)

Refworks - no experience with this one

Labmeeting - I haven't tried this yet since I just came across it but it looks interesting. Drop me a note if you have any experience with this (this promising site appears to have disappeared unfortunately).

Qiqqa (Pronounced "quicker") - Reference and PDF management system. It is Windows based so not as good a system for collaboration as Mendeley.

*There are so many citation/reference management programs available now it is difficult to choose one. Here is a Wiki with info on dozens of options. Personally, I am using Papers and Endnote. I love papers and started with endnote nearly a decade ago and haven't had the time/energy to fully migrate to another program. If I were to start now I'd probably try Mendeley for all of my reference management needs because it's free, open source, available for multiple operating systems, and can sync online so as to avoid being tied to a single computer. There is also good sharing options for lab meetings and collaborative projects. The group at Mendeley also seem to update frequently and really make an effort to improve the product. The only downside is that I've heard it can be slow and the server is unavailable at times.

Here is another link to info on the various PDF and citations managers. It appears that most people are satisfied with what they're currently using. The poll isn't a random sample but the greatest percent of people were using Mendeley.

Another good review of the available options can be found here. One particularly interesting discussion of late has been with the long-term projects of the various options based on their development rates and business models. I would hate to switch to something and then have it die a few years from now. Zotero is open-source and therefore should be available even if not updated in the long term. Also, while I don't mind paying for a good product like Papers, I do feel like the fact that Papers is infrequently updated, isn't free (as in beer), and only available on Mac OS limits its long term feasibility. It's a shame because for the functions it does provide, I find it to be far superior to the other options.

Other Programs