My answer is inspired on my own working experience, and mostly in the book Two Scoops of Django which I highly recommend, and where you can find a more detailed explanation of everything. I just will answer some of the points, and any improvement or correction will be welcomed. But there also can be more correct manners to achieve the same purpose.

Projects
I have a main folder in my personal directory where I maintain all the projects where I am working on.

Source Files
I personally use the django project root as repository root of my projects. But in the book is recommended to separate both things. I think that this is a better approach, so I hope to start making the change progressively on my projects.

project_repository_folder/
    .gitignore
    Makefile
    LICENSE.rst
    docs/
    README.rst
    requirements.txt
    project_folder/
        manage.py
        media/
        app-1/
        app-2/
        ...
        app-n/
        static/
        templates/
        project/
            __init__.py
            settings/
                __init__.py
                base.py
                dev.py
                local.py
                test.py
                production.py
            ulrs.py
            wsgi.py

Repository
Git or Mercurial seem to be the most popular version control systems among Django developers. And the most popular hosting services for backups GitHub and Bitbucket.

Virtual Environment
I use virtualenv and virtualenvwrapper. After installing the second one, you need to set up your working directory. Mine is on my /home/envs directory, as it is recommended on virtualenvwrapper installation guide. But I don’t think the most important thing is where is it placed. The most important thing when working with virtual environments is keeping requirements.txt file up to date.

pip freeze -l > requirements.txt 

Static Root
Project folder

Media Root
Project folder

README
Repository root

LICENSE
Repository root

Documents
Repository root. This python packages can help you making easier mantaining your documentation:

• reStructuredText
• Sphinx

Sketches

Examples

Database

I don’t like to create a new settings/ directory. I simply add files named settings_dev.py and settings_production.py so I don’t have to edit the BASE_DIR.
The approach below increase the default structure instead of changing it.

mysite/                   # Project
    conf/
        locale/
            en_US/
            fr_FR/
            it_IT/
    mysite/
        __init__.py
        settings.py
        settings_dev.py
        settings_production.py
        urls.py
        wsgi.py
    static/
        admin/
            css/           # Custom back end styles
        css/               # Project front end styles
        fonts/
        images/
        js/
        sass/
    staticfiles/
    templates/             # Project templates
        includes/
            footer.html
            header.html
        index.html
    myapp/                 # Application
        core/
        migrations/
            __init__.py
        templates/         # Application templates
            myapp/
                index.html
        static/
            myapp/
                js/  
                css/
                images/
        __init__.py
        admin.py
        apps.py
        forms.py
        models.py
        models_foo.py
        models_bar.py
        views.py
    templatetags/          # Application with custom context processors and template tags
        __init__.py
        context_processors.py
        templatetags/
            __init__.py
            templatetag_extras.py
    gulpfile.js
    manage.py
    requirements.txt

I think this:

    settings.py
    settings_dev.py
    settings_production.py

is better than this:

    settings/__init__.py
    settings/base.py
    settings/dev.py
    settings/production.py

This concept applies to other files as well.

I usually place node_modules/ and bower_components/ in the project directory within the default static/ folder.

Sometime a vendor/ directory for Git Submodules but usually I place them in the static/ folder.

As per the Django Project Skeleton, the proper directory structure that could be followed is :

[projectname]/                  <- project root
├── [projectname]/              <- Django root
│   ├── __init__.py
│   ├── settings/
│   │   ├── common.py
│   │   ├── development.py
│   │   ├── i18n.py
│   │   ├── __init__.py
│   │   └── production.py
│   ├── urls.py
│   └── wsgi.py
├── apps/
│   └── __init__.py
├── configs/
│   ├── apache2_vhost.sample
│   └── README
├── doc/
│   ├── Makefile
│   └── source/
│       └── *snap*
├── manage.py
├── README.rst
├── run/
│   ├── media/
│   │   └── README
│   ├── README
│   └── static/
│       └── README
├── static/
│   └── README
└── templates/
    ├── base.html
    ├── core
    │   └── login.html
    └── README

Refer https://django-project-skeleton.readthedocs.io/en/latest/structure.html for the latest directory structure.

Here is what I follow on My system.

1. All Projects: There is a projects directory in my home folder i.e. ~/projects. All the projects rest inside it.

2. Individual Project: I follow a standardized structure template used by many developers called django-skel for individual projects. It basically takes care of all your static file and media files and all.

3. Virtual environment: I have a virtualenvs folder inside my home to store all virtual environments in the system i.e. ~/virtualenvs . This gives me flexibility that I know what all virtual environments I have and can look use easily

The above 3 are the main partitions of My working environment.

All the other parts you mentioned are mostly dependent on project to project basis (i.e. you might use different databases for different projects). So they should reside in their individual projects.

You can use https://github.com/Mischback/django-project-skeleton repository.

Run below command:

$ django-admin startproject --template=https://github.com/Mischback/django-project-skeleton/archive/development.zip [projectname]

The structure is something like this:

[projectname]/                  <- project root
├── [projectname]/              <- Django root
│   ├── __init__.py
│   ├── settings/
│   │   ├── common.py
│   │   ├── development.py
│   │   ├── i18n.py
│   │   ├── __init__.py
│   │   └── production.py
│   ├── urls.py
│   └── wsgi.py
├── apps/
│   └── __init__.py
├── configs/
│   ├── apache2_vhost.sample
│   └── README
├── doc/
│   ├── Makefile
│   └── source/
│       └── *snap*
├── manage.py
├── README.rst
├── run/
│   ├── media/
│   │   └── README
│   ├── README
│   └── static/
│       └── README
├── static/
│   └── README
└── templates/
    ├── base.html
    ├── core
    │   └── login.html
    └── README