License Dilemma

[Dmitry V. Gorbatovsky]

Dear all
I invent new industrial methodology, in the certain field. It is basicly 
new set of measurements and algorithms of utility optimization based on that 
measurements, available for understanding and use to general public. The 
methodology itself is patentable and patent pending now.

In order to be broadly useful the methodology should be implemented in a
form of computer program. Chosen business model implies development of 
web-application with central multiuser server for application and web-based 
front-end. While most of the functionality of that web-application would be 
available free of charge, I intend to commercialize access to some of it
futures. 

Most of my development environment is GPLed, and I highly appreciate GNU
philosophy and feel that I should use it for good.
But naturally I don't want to compete with another business who just using
my patented method and my own source code against me.
As in later Oracle vs. RedHat story.

Even in case I put a restrictions on commercial use of methodology. It feels 
like any one can brake my business model by doing same thing on the web 
for free.

What is a right approach I should follow.
Please advise. 

Dmitry