To start off, more specifically, what do you mean by systems messages?

There are several applications that can monitor windows behavior inside the operating system, and ways to get around a program showing up in the Task Manager such as using a rootkit method that Sony has recently made headlines with.

Even VMware has a host operating system that is was developed for. I would find the attempt to develop a similar program, let alone one that isn't noticeable to an end user, to be an enormously challenging task.