As far as I know, I am one of the few, if only, Linux users in the faculty on my campus. This comes up from time to time, often when someone walks by my laptop and doesn't see the usual Apple/Windows interface. I have discussed Linux with some of my colleagues; many are interested in how I do the things I do with it for school.
This is a list of Back To School apps for faculty who use Linux. I use each of these on a day to day basis and I would not be as productive as I am without them. Good news for Windows/Apple users: Many of these are cross-platform applications you can use too.
Tomboy: Tomboy is my note taking program of choice. I have a variety of uses for Tomboy: I keep a "to do" list that also loads on Conky (see below) plus numerous notes for each day of the week, ideas for projects, and other assorted randomness. The biggest use as a faculty member for me is having portable notes with lists. I have a pre, and post, semester list. I have a running list of things that need to be added to my annual report. In the summer, I draft and map my classes for the year via Tomboy notes. Tomboy can be synced over a number of computers via the cloud or, what I do, by syncing the folder my notes are in over a number of computers using Spideroak (look down).
Spideroak: I moved to Spideroak about a year ago after issues with a few of their competitors. Spideroak is an extremely secure backup program (see the Security Now! podcast episode about it) that backs up your work and can be synced over a number of devices. It is also cross-platform. I use Spideroak on my home desktop (Linux Mint 15), the laptop I bring to work (Ubuntu 12.04), another laptop running Ubuntu 11.10, and my Android phone and tablet. I can also access it via the web on my office desktop (which I run using Portable Apps...see below) One caveat: You cannot upload files to your Spideroak archive from the web ala Dropbox. I have been told by someone at Spideroak this is for security reasons.
Calibre: Calibre is an ebook manager that can also swap your books between various formats. Depending on your ebook reader, you may want books in .mobi, .ebook, or PDF (I had a student this summer who had a Nook, I think, and wanted everything in PDF) or a multitude of other format options. Calibre lets you transfer between these formats with relative ease to keep up with wherever your books are going.
Conky: Conky is a lightweight system monitor that allows a user to visually display information from their computer. As I said above, I use Conky to display my task list from Tomboy. I also display a monthly calendar, my daily Google Calendar, and various information about what is going on within my computer (CPU. Memory, What Song is Currently Playing). Conky is fairly easy to set up, UbuntuForums have a number of tutorials that users have created, although you don’t have to be a user of Ubuntu (personally I run Linux Mint for the most part) to use them.
LibreOffice: LibreOffice is a great alternative to Microsoft Office that I use on a day to day basis. Many of my students, not willing to put down the amount of money Microsoft wants for their products, also use LibreOffice. LibreOffice allows users to create documents, presentations, spreadsheets, etc. I have used various forks from this project for about 10 years and have never looked back at Office. It’s not perfect, but good enough for me.
Portable Apps: While not Linuxcentric, I use Portable Apps on my work computer a lot to make sure I can use the programs I want. I do trust my IT Department and like them a lot, but I am not that interested in using Microsoft Office or Internet Explorer. I carry a flash drive in my bag with Google Chrome, LibreOffice, and a handful of other programs. I also run HTTPSEverywhere in Chrome to make sure my connections are secure on our Wi-Fi Network.
Linux Boot Drive: Even if you are not a Linux user, I think every academic should have a copy of some form of Linux on a flash drive or CDR. Most forms of Linux allow you to run a "live" version of the OS before you install it. Normally, users would use this to test compatibility and make sure hardware and drivers (I had a laptop years ago that had problem with the rather infamous Broadcom wireless cards) work in Linux. However, this can also be used to, potentially, recover files from a broken Windows system. Say your Windows XP laptop crashes. Depending on how your OS failed, there is a decent chance your files are fine. Booting into Linux could allow you to recover your files before reinstalling. Of course, this is why you should be backing up (see above).