Q:

What are the files with a com prefix

I've seen many files start with a com on my machine, eg. com.apple.mail, anybody know what is the com stands for?

A:

This style of naming is a common practice (mostly in Java) to help give code packages a unique namespace to avoid naming conflicts in programming. 
The standard specifies that the namespace begins with a top level domain, with the inverse of the domain name of the company distributing it being common practice. That is, if the package is produced by example.com, its unique namespace might look like com.example.unique.module.
So, as pointed out in the comments, it means the same thing as it normally does at the end of a domain. It is simply being used for a different purpose.

