At some bigger studios where I've worked, we use a production tracking system system called Shotgun. It helps the supervisors and crew manage scenes, assets, schedules, reviews, comments, etc. That may be overkill for many smaller and indie productions though.
At smaller studios (and even some big places) where I've worked, we just used a spreadsheet or simple database system.
For my
personal projects, I use either LibreOffice and store the files in a cloud storage service like Dropbox or Google Drive, or I'll use GoogleDocs and GoogleDrive. This way I can access the information from any computer, whether I'm working on the project at home or away. The system works well for me because I have control over how it's set up, because it's easy to use, and it's cheap as free.
Here's an example of a 'scene tracker' I helped my daughter set up last fall for a short film she made. We created it in GoogleDocs. She had storyboarded almost 30 scenes for her film and this list helped her understand the status of each scene at any moment and what she still needed to do to complete her film.
The way this spreadsheet works is simple: The scenes are listed from top to bottom, and the tasks from left to right. As she completed each task, she checked it off. Over in the Status column, the number increased with each check box for that line and the color changed from red to yellow to green. At the beginning, the column was completely red and by the end of the project, she had turned the column completely green as seen in this example.
My daughter found this 'checklist' system very gratifying because it gave her a clear understanding of the scope of her project, helped her plan her time, and see the progress she was making. I should point out that she was 11 years old at the time and, even though she's been making animated shorts since she was 7, this was her most ambitious project to date, and having the 'checklist' really helped her focus on what was needed to get it done. (Here's a link to her finished film if you're curious:
Class Act)
This system is actually not that different from what I use in my own personal projects. My own system may track a bit more info, especially when I'm working with other artists, but it's the same idea. As a matter of fact, even though the studio where I work has a sophisticated production tracking system in place, I still create my own personal spreadsheets to track my assignments in addition to the studio system. For me, it's a good way to manage my own notes and progress without a lot of 'extraneous' information getting in the way.
I hope this helps.