Computation of the fundamental group of $X=\mathbb{R}^3\setminus (C_1\cup C_2)$, where $C_1$ and $C_2$ are two disjoint linked circles.
We apply the van Kampen theorem.
Let $U$ be the open halfspace to the left of the green plane, and $V$ be the open halfspace to the right of the blue halfspace. Fix the basepoint $x_0$.
Clearly $\pi_1(U)=\pi_1(V)=\mathbb{Z}*\mathbb{Z}$, as both $U$ and $V$ deformation retract to $S^1\vee S^1$. Similarly, $\pi_1(U\cap V)=\mathbb{Z}*\mathbb{Z}*\mathbb{Z}*\mathbb{Z}$, as $U\cap V$ deformation retracts to $S^1\vee S^1\vee S^1\vee S^1$. Let $p_1$ and $p_2$ be homotopy classes of loops in $\pi_1(U\cap V)$ encircling the missing arcs in $xy$ plane, with $p_1$ corresponding to the arc with positive $y$. Similarly $q_1$ and $q_2$ are classes of loops encircling the arcs in $xz$ plane with $q_1$ corresponding to the arc with positive $z$. Thus $p_1,p_2,q_1,q_2$ are generators of $\pi_1(U\cap V)$.
Let $i:U\cap V\hookrightarrow U$ and $j:U\cap V\hookrightarrow V$ be the inclusion maps. We might clearly take $a=i_*p_1$ and $b=i_*q_1$ as generators of $\pi_1(U)$ and $c=j_*p_1, d=j_*q_1$ as generators of $\pi_1(V)$. The amalgamation product tells us that $i_*r$ should be identified with $j_*r$ in $\pi_1(U)*\pi_1(V)$ for all $r\in \pi_1(U\cap V)$. Thus $a=c$ and $b=d$, so we reduce $\pi_1(U)*\pi_1(V)$ to $\mathbb{Z}*\mathbb{Z}$. But there are more identifications we need to take into account, in order to obtain $\pi_1(X)$. Observe for example that we must identify $i_*p_2$ with $j_*p_2$. But $i_*p_2=a$ and $j_*p_2=dcd^{-1}$, so $a=bab^{-1}.$ So we further reduce $\pi_1(U)*\pi_1(V)$ to $\mathbb{Z}\times \mathbb{Z}.$ One more identification needs to be taken into account, but it does not give anything new. Thus $\pi_1(X)=\mathbb{Z}\times\mathbb{Z}$.
$\mathbf{Another}$ approach is to use cover by the opened sets as on the next figure.
It is easy to see that $\pi_1(U)\cong\pi_1(V)\cong\mathbb{Z}\times\mathbb{Z}$ as they both deformation rectract onto a torus. Moreover, as in the previous situation, we see that we may identify the generators of $\pi_1(U)$ and $\pi_1(V)$ in the amalgamated product, via generators of $\pi_1(U\cap V)$. Thus $\pi_1(X)=\mathbb{Z}\times\mathbb{Z}.$
Similar, but easier arguments, could be employed to show that $\pi_1(\mathbb{R}^3\setminus\text{circle})=\mathbb{Z}$ and $\pi_1(\mathbb{R}^3\setminus\text{two unlinked circles})=\mathbb{Z}*\mathbb{Z}$.

