I think most of us (including myself) massively underinvest in finding and learning good tools. It's one of those things where the upfront costs to finding/switching tools are large and annoying, but the long-term benefits are astounding if you can actually get round to it.
Here's a list of tools I use and that have generally worked well for me, although in some cases I think there might be better ones out there (I'd love to hear about them). If there are other tools you love I'd obviously love to hear about them too – a lot of great tools fill gaps that you didn't exactly know you had.
Online Word Processing: Quip and Googledocs
Online word processing is just ridiculously useful and convenient, to the point where I'm always a bit shocked to discover now that there are people still using Word or whathaveyou of their own free will.
There isn't yet a "perfect" online word processor I know of but the two I use regularly are Quip (shown above) and GoogleDocs. Both are free. It's obviously a bit of a judgement call, but I think Quip is overall the better application right now (as of summer 2015): it's hard to explain exactly but some combination of the commenting and chat features and the speed of loading and the look of the thing make it the online word processor I use when I get the choice.
That said, Googledocs' Docs (they should really name that thing) is also very good and much more well known/commonly used. I probably end up using Googledocs more often because that's what friends and collaborators are more familiar with, and Quip isn't really better-enough that it feels worth the hassle of asking/begging/cajoling anyone to switch for my convenience.
Not everyone seems to know that Googledocs has an offline version which lets you keep editing your documents even when you don't have internet connection; this used to be a bit buggy (I once lost an important document because Googledocs over-wrote my offline text when I went back online, and Google support seems to be essentially non-existent) but to my knowledge it now works just fine.
I previously used:
Draft, really simple markdown-based online text editor. Reluctantly not recommended, I really liked the concept and it's a one-man shop that I wanted to support but I feel like it's not really being maintained up to the standard necessary.
Penflip, online text editor with emphasis on version-control (being able to access all previous versions of a document, and seeing the differences between versions easily). Not sure why I stopped using this one, nothing specific wrong with it, I guess I just like Quip better at this point.
Listmaking and Organising and Other Things: Trello
Trello, free list-making and list-organising software. It's a little hard to explain why this is so frigging useful, but actually the founder of the company explains it really well: the most crazily-successful general-purpose software applications, he says, are generally built on single data structures. For example, spreadsheets are all about making tables of stuff; "Most Excel users never enter a formula. They use Excel when they need a table. The gridlines are the most important feature of Excel." Word processors are all about "lines of text which automatically wrap and split into pages." Ok, so what's Trello?
Some people saw Trello and said, “oh, it’s Kanban boards. For developing software the agile way.” Yeah, it’s that, but it’s also for planning a wedding, for making a list of potential vacation spots to share with your family, for keeping track of applicants to open job positions, and for a billion other things. In fact Trello is for anything where you want to maintain a list of lists with a group of people.
It's hard for me to express how many times I want to solve some organisational problem and the best answer turns out to be "make a list of lists that you can move cards between."
Spaced Repetition/Memory: Anki
Anki, free spaced repetition software. Based on really impressive research about how your brain learns things better with repeated exposure: you put a fact/question/answer into Anki and it shows it to you again at fixed intervals that are optimised to make sure you actually learn and remember the information for the long term.
This excellent article by Sue Shellenbarger was a lot of my inspiration for starting to use this properly in my everyday life. I really, really wish I'd discovered it while I was still a student.
Offline Word Processing: Sublime Text
Sublime Text Editor is a word processor for coding and writing. Free trial with no fixed trial period (you will only get occasional popups asking if you'd like to buy, but you're under no obligation and the trial is not time-limited). Mind-blowing search and organisation features.
I previously used:
Mou, Markdown editor. Free download. Simple and light-weight. Now largely replaced with Sublime, sometimes use it when I want to jot some notes.
TextWrangler, lightweight coding editor. Free download. No longer use at all, replaced with Sublime.
Version control (for coders): Github
For most people this isn't relevant but if you're starting to learn computer programming, get started with Github as early as possible (I say). I avoided it for a long time because it looked too intimidating but with the desktop app (and while you're doing one-person projects that don't require merging and such) it really is as simple as pressing some buttons and it's incredibly useful when you screw up your code and want to go back to a previous version.
NOT RECOMMENDED/ Still looking for something good
Wiki-making, knowledge bases
NOT RECOMMENDED: Confluence, Wiki and other collaboration tools for teams. $10/month. Was recommended by some friends but after several months of use I realised I just didn't find it helped as much with organising tasks as I had hoped, and it was INCREDIBLY (painfully, unbearably) slow when switching between pages, making it really unpopular with my collaborators and so largely useless to me.
I've largely replaced Confluence with GoogleDocs and Quip – they're not wiki-specific, not really built for the purpose, but with a few inbuilt links or organised documents they can achieve the same goals. And they're both free, and they're both fast.