This is the set up I've used during my undergrad/Masters and that I'm going to carry through onto the PhD.
I'm using a whole bunch of different tools to streamline my work and offload my brain - I have a goldfish memory (the castle around the corner is a surprise every time!*) and tend to worry about everything. All the time. I can't be very efficient without knowing that I can "forget" certain things because they have been recorded somewhere (and that I will get a reminder when the time comes).
The ease of recording things, as well as the ability to access the information is paramount, as I work from several locations and need to be able to get my hands on all that data anytime, anywhere. I need a set up that will not only work between office and home, but also between 4 different countries on 2 different continents. Something that will work cross-platform, as I use both a tower PC and a MacBook, as well as an iPad and an Android phone.
I am currently using:
The Trio of Skim, Scrivener and LaTeX - Skim for reading and marking scientific papers, Scrivener for the bulk of my writing, including notes taken on the papers all the way to, hopefully, the Thesis. LaTeX is my secret weapon of choice when it comes to formatting, it's really second to none in this category.
Mendeley - for keeping track of my references. It produces a bibtex file that can be used with LaTeX to automatically input and format references, both in text and at the end of the document as a bibliography.
For keeping track of most of my life I'm using Calendars (used to do Google, but swapped to iCloud now for no real reason), Evernote and Wunderlist. Each of those plays a slightly different role, Calendars organise my day/week/month, Evernote collects things that might be of use one day (meeting and lecture notes, recipes, manuals, travel arrangements, blog ideas…), while Wunderlist is there, well, to keep track of my multiple to-do lists and my daily agenda.
Mailbox - I have also recently started using Mailbox on my iPad and Android in order to achieve "inbox zero". I wasn't sure I will likely, but I'm totally digging it.
I'm also using Bloglovin' and Pocket to read things that are not scientific papers. Bloglovin' keeps track of all blogs (I read mainly academia/science-related blogs). Pocket is the "I'll read it sometime later" bucket, where I throw stuff that might be interesting, but that I'm not sure I want to keep - if I do want to keep it, it will probably end up in Evernote.
I am still working on my cross-platform links, as an iPad is a fairly new addition to the family - I was lucky enough to win one in a contest and so haven't been building those systems with an iPad in mind. I am also attempting to use IFTTT to automate some processes, but I think I have a long way to go here.
I am going to write a separate blog post on how I'm using each of the above, in case anyone out there is curious, but also so that I can see how my habits evolve over time. Once the posts are written I will link to them in this post (probably make the names of the programs clickable too).
*I'm pretty sure I have heard this somewhere, but for the life of me can't remember where.