I've recently used 3 programs:
All of them allow you to create chapters and scenes, where each scene is stored in it's own separate document, which allows you to arrange those scenes any way you like.
Manuskript:
-I really likes this program. it has more features than ywriter, but it's also a little more cluttered.
-free
-distraction free mode with nothing but the page in front of you.
-cork board.
-You can track sub plots and then view them along a timeline at the bottom to see which chapters they show up in, although adding a subplot is a little unintuitive. (it took me an hour to figure out how to do it)
-you can create characters, plots and world items and then assign them to your individual chapters.
-Spell check is built in and actually works.
-multiple editor tabs, and you can split the editor into many different windows to view more than one document at a time.
-There is a bug where the program wont launch if you are using windows dark mode, which was a pity
-No rich text, (that I could find) so you can't add italics etc
YWriter:
-free
-Clean, simple interface. Keeps track of your characters, items, and locations, and you can then tag those to your various chapters. The downside is that there is no built in tool for tracking subplots. You have to add a subplot as a character or an item, as a workaround, in order to track them.
-you can add notes, images, times and dates to each scene.
-There is an android / ios app that you can buy for $5, that allows you to sync up your writing with your mobile device.
-It allows you to add a start and end date as well as the final word count and it will then keep track of how many words you need to write every day.
-I couldn't get the spellcheck to work no matter what I did.
-basic rich text allows you to add italics etc
-no dark mode as far as I can tell, and it doesn't respond to windows dark mode settings either.
Scrivener:
clean and powerful. This is a fantastic program that can do everything, including exporting as a mobi or epub, but of course it isn't free.