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For Nicolas' particular cases:

"More subtle:

dx/dt = k * C * Y / (K + Y)
where C = [calcium/calmodulin]/[total calmodulin]

You would declare A as a modifier

but

dx/dt = k * P * Y / (K + Y)
where P = pH

You would not declare P as a modifier, but as a parameter

Even if pH is in fact proportional to the concentration of H+"

In the case of the reaction controlled by calcium:CaM, yes I would definitely expect calcium:CaM to be a species and to appear in the ListOfModifiers.

In the case of the pH-controlled reaction, if H+ is in the ListOfSpecies, but not in the lists of Reactants or Products for the reaction whose kinetic law you have written, then I WOULD declare H+ as a Modifier even if P were defined by

P = -log[H+]

If P is constant, then yes it could be a parameter, but I imagine most people would lump it into the rate coefficient, k.

In the case of the assignment rule:

"Consider the following assignmentRule:

species A
parameter X (not an entity pool)
parameter Y

if CONDITION 1
then Y = A
else Y = X

What is Y? "

I don't think Y can be identified as a reactant, a product or a modifier.