I am an ecology post-doc and considering switching from Windows to Linux for my main work computer (I am not a mathematical modeller). I have used Linux before and I am aware that, with effort, one can accomplish most any task in Linux that one can in Windows but I have not tried to convert my whole work computer over. And sometimes making a specific type tool/application work or share files with colleagues' tools (likely Windows based) can take a lot of effort/time or be error prone. As academics we all have limited time to troubleshoot issues that might appear optional.
So, my question here is for people who have made this switch or seriously considered it: what are the specific main challenges you encountered (which types of applications/tools or other issues) in making this switch?
I'm especially interested in word processing, spreadsheets, databases, statistical software, plotting and presentation software, reference management, communication, and any other applications that allow you to fulfill key responsibilities as biology faculty. I know there are various ways to port/emulate/etc Windows applications into Linux (e.g., Wine), but I'm interested in approaches that don't simply use that for every application I'm used to in Windows. And I'm asking about what challenges you had transitioning (or why you choose not to) rather than just asking for a list of Linux applications that fulfill these needs (that said, do mention specific applications if you think they are less well known).
(I'm trying to keep this narrow and not about the benefits of either OS over the other - no need for a Linux/Windows flame war. I've also tried to prevent this from being an opinion oriented question by asking for specific problems, but please let me know if I should modify to improve further).