Being an academician and techie, I often come across the question of “I’m starting my research… can you suggest some apps that will help me?”
Here are some software that I would personally suggest you to try out. Please note that the list is incomplete and I will be updating it in course of time.
Docear (Discontinued)
When it comes to citation management, there are tonnes of applications like Zotero, Mendley which does the job neatly. I have, all my life used MindMaps as a tool to organize my thoughts and may be that’s why I found Docear more interesting than others. But unfortunately, like many other open source projects, Docear is discontinued as they “do not have the funding and time to continue the development of Docear, or giving support”.
Almost all functions of Docear are available in XMind, including pinning a document to a tree. But XMind is not free; though the 1-year free trial is worth the shot.
If you would like to stick to FOSS; FreeMind (Discontinued; Buggy) and FreePlane (Forked from FreeMind; usable) are also very good MindMapping alternatives, though a lot limited.
Google Keep or SimpleNote
I have also been fascinated by the simple yet powerful tagging system in these two not-taking apps – which can double as information management systems for us. Both supports Rich Text. My dad uses Keep to manage information for his book on religion, and he finds it pretty useful.
I personally has been using Keep as a diary to record all work-related activities categorised by its nature and date.
Automattic’s SimpleNote also supports Markdown Markups, and that comes in handy at times, if you’re more used to typing in text.
The reason I started writing this article is the following web application:
Gingko
FOSS – Free/Paid Upgrade for Heavy Users
I came to know about Gingko only an hour ago – but fell in love with it ASAP!
They call it “a tree-based Word Processor” – it’s almost mind map, but for longer articles/writings/novels. It supports MathJax, hence math typing is no trouble. That means, if mastering Markdown Markup Language is not a trouble (widely used in many websites already including StackExchange), this tool is a boon to any kind of writers alike, be it a novel or a textbook or a thesis.
I also tried the export feature and I must say that the document I exported to MS Word had Styles almost properly applied. Plus, it has an option to export document in various other formats, including 
The ideal writing companion I had in mind.
The paid version is not costly either. You can pay as low as $2 a month to $21 a month (your choice!), else you are restricted to 100nodes/month.
Nulis.io
FOSS – Website
Nulis was inspired by Gingko and free. Worth a shot. Writing Streak is another project by same developer; do check them out as well.
Sign Up for free with following link to get extra 100 cards per month.
This list is incomplete and will be updated as I come across more useful tools. Note that these are my personal recommendations and better tools does exist, most of which are paid.
Mathematicos 
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