Let's assume a radius of $1$.
As you say, in the first case, the length of the fence is the radius, $1$.
In the second case, though the fence is the diagonal of a square, it's not evident whether the top right corner of that square is inside or outside the circle, so you can't conclude from that alone that the fence is longer than the radius in this case. The area of the triangle is $a^2/2$, where $a$ is the length of one of its legs, and the length of the fence is $\sqrt2a$. The area must be $\pi/8$, so $a^2/2=\pi/8$ and thus $a=\sqrt\pi/2$, and the length of the fence is $\sqrt2\sqrt\pi/2=\sqrt{\pi/2}\approx1.2533\gt1$, as you suspected.
In the third case, you're right to conclude that the fence is shorter than the radius, so this is the shortest of the three fences.
However, that doesn't tell us whether this is an optimal fence. In fact it probably isn't, since you can tilt the fence sideways a little to make it hit the circle earlier, then move it to the left a bit make the two areas equal again.
A fence that meets the quarter-circle twice can't divide the area in half, so the fence has to either meet both straight edges or one straight edge and the quarter-circle. It's well-known that the diagonal fence is the optimal solution for the first case, and we've already shown that that's not optimal, so we can conclude that the second case has to obtain; the fence has to meet one straight edge and the quarter-circle. Without loss of generality, assume that the straight edge that it meets is the bottom one, as in your third figure.
Let the optimal fence meet the quarter-circle at $\def\yopt{y_{\mathrm o}}\def\xopt{x_{\mathrm o}}(\xopt,\yopt)$. Then the area under the quarter-circle up to that point is
$ \begin{eqnarray} \int_0^{\xopt}\sqrt{1-x^2}\mathrm dx &=& \frac12\left(\xopt\sqrt{1-\xopt^2}+\arcsin \xopt\right) \\ &=& \frac12\left(\yopt\sqrt{1-\yopt^2}+\arccos \yopt\right)\;. \end{eqnarray} $
Let the slope of the fence be $1/a$. Then the area of the triangle under the fence is $\frac12a\yopt^2$. The difference of these two areas must be half the area of the quarter-circle, that is, $\pi/8$:
$\frac12\left(\yopt\sqrt{1-\yopt^2}+\arccos \yopt\right)-\frac12a\yopt^2=\frac\pi8\;,\\ a=\frac{\yopt\sqrt{1-\yopt^2}+\arccos \yopt-\frac\pi4}{\yopt^2}\;. $
The square of the length of the fence is
$\yopt^2+(a\yopt)^2=\yopt^2+\left(\sqrt{1-\yopt^2}+\frac{\arccos \yopt-\frac\pi4}{\yopt}\right)^2\;.$
The optimal fence is determined by minimizing this expression with respect to $y_0$. I doubt there is a closed-form solution for the minimum; Wolfram|Alpha finds the minimum at $\yopt\approx0.854563$, and thus $x_0\approx0.519348$ and a squared length of approximately $0.787547$, which yields an optimal fence length of about $0.887438$. For comparison, the length of the vertical line in your third figure, which corresponds to the case $a=0$, is the solution of the equation $\yopt\sqrt{1-\yopt^2}+\arccos \yopt-\frac\pi4$, which Wolfram|Alpha says is about $0.914771$, not that much worse.
Here's a diagram of the optimal fence. This problem might serve as a warning not to assume that an optimal solution shares the symmetries of the problem (which I would have had a tendency to do in this case).