Note that $y=x^2$ is an equation, to be more precisely a statement form. It states: “The second coordinate is the square of the first one.” For the coordinates of a point that statement may be true -- for $(-2,4)$, e.g.-- or false for, say $(7,50)$. The set of points for which the statement form yields a true statement is called the solution set of the statement form. The statement form $y-x^2=0$ states: “The difference of the first coordinate and the square of the second equals zero.” is a different statement form, but has the same solution set as the first one.
The second one is given in a so called implicit form, wheras the first is called an explicit form. Why bother about the to forms? Well, if you want to determine the second coordinate of a point in the solution set, given the first coordinate is $7$, let's do it using the imlicit form. We have
$$y-7^2=0\iff y=49,$$
so you have to solve an equation. (That's the reason for why we call it implicit.). Using the explicit form we get immediately $y=7^2=49$ without solving any equation.
Your first example $y=1/x$: “The second coordinate is the reciprocal of the first one.” reads in implicit version $xy=1$: “The product of both coordinates equals one.” Another explicit form is $x=1/y$. So if you are able to isolate one coordinate in an implicit form, this coordinate is called dependent, the other independent. In $x=1/y$ the coordinate $x$ is dependent and $y$ independent whereas in $y=1/y$ it's vice versa.
Now in $y-x^2=0$ you can't isolate $x$ in a closed form, here we have $\sqrt{y}=|x|$. So if for example $y=25$ we have $\sqrt{25}=|x|\iff5=|x|\iff x=5\lor x=-5$, so we have to solve an equation anyway. You may write $x=\pm\sqrt{y}$ and see that for all positive $y$ you'll get two values of $x$, so that explicit form is not a function, which mathematicians prefer.
In the example $x^2+y^2=1$ given by James there doesn't exist any explicit form which is a function, for an obvious reason: the solution set is the unit circle, centered at the origin.
Facit: if a statement form allows an explicit form of one of the coordinates and that explicit form is a function, you are free to call the isolated coordinate dependent and the other independent. I never use those attributes, because they are rather useless, won't gain any knowledge and are causing a lot of trouble as we see here.