Partially completed theme.What should a decent or usable worpdress theme have?

You might want to review Theme Development for some ideas.

Yes, I have been referring that documentation.

I need to know, like the themes such as twenty twelve, twenty thirteen, twenty fourteen; should I have to write and include separate comments.php,404.php etc, files in the package, or can I simply include the part of the code in the single.php or any other file where it will be executed?

For ex: Comments appear below a single post , therefore I have written the comments_template(); function in the single.php.

But in the themes like twenty twelve, twenty thirteen, twenty fourteen, there is a separate file for comments.php.

What practice should be followed, a separate comments.php or combined with single.php?

I suggest reading Template Hierarchy to understand what files WordPress looks for and the consequences of not having a certain file included in your theme.

In your particular case, you technically only need comments_template() in your single.php. WordPress will use a default template to display comments. However, if you’d like to further customize how WordPress will display comments, you can create your own comments.php in your theme directory and WordPress will load that file instead.

Thank you that template hierarchy was the document I was searching for.