Microsoft Word (Windows and Mac)
I primarily use word to write up my first drafts and to edit other people's work. It's really good for long bodies of text. Annotations are hard to make and keep track of, but pressing 'Ctrl+F' will get you the search tool, which you can use to find exact phrases or words. It's good to see everything you're writing in one mass, and how it will flow. Also, if you're preparing to print out your manuscript onto a hard copy, it's really easy to see how it will look.
If you are using it to edit, it has highlighters and commenting tools. These are the ones I use most often to edit, and it's a good, clear visual way of editing.
For typing it up, personally I recommend size twelve font and in something easy to read, because it make sit a lot easier to see and read through. But it's more personal preference, whatever works for you.
Microsoft OneNote (Windows only)
OneNote is really good for keeping track of different parts of your manuscript. I mainly use it for when I get ideas for different snippets, or piecing together different parts of my story if I don't think of them in consecutive order. It's also really good for writing down outlines and other story plotting things and keeping them in one place. It's like a notebook you can write different things in different pages, except on computer so it's easier. In fact, I use OneNote to manage my blog posts!
Microsoft PowerPoint (Windows and Mac)
I only use PowerPoint for one thing- character profiles. It's like a flipbook of characters, where it's easy to put in photos and a smile amount of information so you can easily flick through and see it. Of course, elaborating on your characters in OneNote is always a good idea, because you can only fit so much in a PowerPoint slide.
Scrivener (Windows and Mac)
This is a new one for me; I only just found it. From what I've seen so far in the tutorial, there are lots of functions that would be handy for editing and going through your story. It also has lots of options for sorting through things and annotating so you're super on top of your story and know it back-to-front. It has heaps of different functions for writing different things including scripts. As I said, this is new for me, but it looks really handy and clever, and I'd love if you came on the Scrivener journey with me! You can download the free trial or purchase it here- http://literatureandlatte.com/scrivener.php
So those are the applications I use most often and I find most handy for writing, but please keep in mind that everything with writing is a personal choice, and it's up to you to figure out how you want to write. Personal preference is key! Also, I am no professional, I'm not even a published author, I'm merely sharing my experiences and things that I find make writing easier, so please don't think my writing is gospel.
I hope you found this helpful and keep writing! Also, share any tips you have down in the comments with your twitter name and I will shout you out!