When a user buy a software and enter a serial number, it is registered to the user? right?
If yes, what is the proposition for the Register
This program is registered with/to/for XXX company.
Yes, we generally say that the product is registered to the user who bought it. If you're talking about the company that sold the software, it would be more normal to say that the program is registered with the company. For example, "Customers must have all Red Hat software registered with Red Hat to qualify for the warranty."
By the way, software is a mass noun or uncountable noun, so you can't say "a software". Use "software" to speak of software in general, or "a program" if you need to talk about a specific example.
There can also be the use of "by" to denote who handles the registration process.
This program is registered by XXX company.