We have the following statement: "The final 3D effect is realized by a combination of the native 3D effect and a shadow effect". Is it all right to say "realized by ..." or should it be "realized with ..."?
I think Maciej's answer is correct but it is stated rather specifically: the abstract principle is embedded in a concrete example. Here is the abstract principle:
Since by denotes instrumentality, it partners semantically with an action, here combining:
The final 3D effect is realized by combining the native 3D effect and a shadow effect.
Paraphrase: The native 3D effect and a shadow effect are combined in order to produce the final 3D effect.
Since with denotes participation or involvement or agency, it partners semantically with a noun that participates in or is involved in or is a co-agent in an action:
The final 3D effect is realized with a combination of the native 3D effect and a shadow effect.
Paraphrase: The final 3D effect is a result of using the native 3D effect and a shadow effect.
P.S. To complicate matters, the abstract ideas of instrumentality and participation/involvement/agency can shade into one another. The complement of with can be an instrument, co-actor, or co-agency:
I chopped the tree down with this axe, said George.
We did it with their help.
The dentist repaired the tooth with his dental assistant.
But we would not say realized with combining.
And sometimes the underlying verb of nouns like combination will cause speakers to use by with the noun:
The final 3D effect is realized by a combination of the native 3D effect and a shadow effect.
That last sentence strikes my ear as somewhat "off" because the action of combining is not immediate but one step removed. There is a forced "cast":
by (verb) noun
If the effect is realized with a tool, it means that someone or something is utilizing the tool to create the effect, while if the effect is realized by a tool, it means that the tool is creating the effect itself.
In the context you mention, I'd say they're more or less interchangeable - I'd lean towards "realized with" when focusing on an artist or game developer applying the effects to create the final product, and "realized by" when focusing more on the product itself.