If you already keep your computer files fairly reasonably organized, that's great (this section may not be for you). If you instead do a little of this, a little of that...and have to frequently hunt around for stuff you need: "Which folder? Which drive? 'Assignment Two'? But WHICH COURSE?? Dang; this desktop has got SO MUCH STUFF on it., I have to deal with this one of these days..." then these tips are for you.
You have folders. Use them. However, don't set them up based on someone else's way of organizing their information - think about how YOU categorize information, so you can set them up so that when you go to look...it makes sense to you.
Folder names - again, what makes sense to you. Bit boring, but class name or number and sub-folders for units or assignments inside seldom goes wrong.
Naming individual files: this may be the most important tip for keeping your computer files so that they don't drive you to distraction later. You have to create a 'naming convention' for how you title those files / documents, that makes sense to you , that tells you enough about what the file is - and do it consistently.
By the way, if your degree area involves research? By developing good file naming habits, you'll be ahead of the game (since part of being a responsible researcher is having good data management habits).
Speaking of data management, you'll need a way to back up your information, at least until you really no longer need it. Our IT student FAQ also warns you about backing up your personal laptop files.
Read it here: "Why should I back up my data"
The last item is: culling files when you really no longer need them. (Don't jump the gun on this one, though - assume Murphy's Law will kick in if you delete them at any point before you've received the final grade for that class.)
That said, also have a system for deleting truly unnecessary files - even if just once a year. And yes, some files can be kept longer-term, and some deleted fairly quickly as well (such as random notes or snippets of info no longer needed for that assignment turned in last semester).