So let $\Gamma\subseteq SL_2(\mathbf{Z})$ be a finite index subgroup (not necessarily a congruence subgroup). Recall that we have an action of $SL_2(\mathbf{R})$ on 
$\mathbb{H}=\{z\in\mathbf{C}:\Im(z)>0\}$ by moebius transformations and therefore of $\Gamma$. If $\tau\in\mathbb{H}$ and $[a,b,c,d]=\gamma\in SL_2(\mathbf{Z})$ then we have an isomorphism
of complex tori
$$
\mathbf{C}/(\mathbf{Z}+\tau\mathbf{Z})\rightarrow \mathbf{C}/((a\tau+b)\mathbf{Z}+(c\tau+d))
\mathbf{Z}\rightarrow (\mathbf{C}/\mathbf{Z}+\gamma\tau\mathbf{Z}) \;\;\;\; (*)
$$
where the first map is the identity and the second map is the multiplication by $(c\tau+d)^{-1}$. Let
$$
\tilde{\mathcal{E}}_{\Gamma}=\{(\tau,x):\tau\in\mathbb{H},x\in \mathbf{C}/(\mathbf{Z}+\tau\mathbf{Z})\}
$$
We have a natural left action of $\Gamma$ on $\tilde{\mathcal{E}}_{\Gamma}$ given by
$$
\gamma(\tau,x)=(\gamma\tau,j(\gamma,\tau)^{-1}x),
$$
which is just a reinterpretation of $(*)$. Here $j(\gamma,\tau)=c\tau+d$. We thus get the following family of curves (note that the fibers are not necessarily elliptic curves because of the presence of torsion in $\Gamma$ as K. Buzzard pointed out):
$$
\pi_\Gamma:\Gamma\backslash\tilde{\mathcal{E}}_{\Gamma}=:\mathcal{E}_{\Gamma}\rightarrow Y_{\Gamma}:=\Gamma\backslash \mathbb{H}
$$
In the case where $\Gamma$ is torsion free, we readily see that the fibers are elliptic curves and the the $\Gamma$ action is compatible with the addition on the $tori$ (this somehow justifies the terminology "universal elliptic curve" over $Y_{\Gamma}$).

In general one always has that $Y_{\Gamma}$ is a quasi-projective curve defined over $\mathbf{C}$ (in fact it is always possible to define this curve over $\overline{\mathbf{Q}}$, the algebraic closure of $\mathbf{Q}$). 

[For example, when $\Gamma=\Gamma_0(N)$ one may look at the modular polynomial $f_N(x,y)\in\mathbf{Z}[x,y]$. Then using the modular interpretation one can show that there exists a (complex analytic) immersion of $Y_{\Gamma_0(N)}$ onto the plane curve $C_N: f_N(x,y)=0$. If I remember correctly, in the finite chart $\mathbf{C}^2$ (for $N$ large enough) the singularities of $C_N$ are nodes and thus one can blow-up these points (over $\mathbf{Q}$!). From this one can construct a complex analytic isomorphism between $Y_{\Gamma_0(N)}$ and the blow-up (which is quasi-projective curve defined over $\mathbf{Q}$.]
 
So here are 2 natural questions.

**Q1**: Is $\mathcal{E}_{\Gamma}$ quasi-projective (at least when $\Gamma$ is torsion free)?

**Q2**: If the answer is yes, then what is the **cleanest** (and if possible most transparent) way of showing that $\mathcal{E}_{\Gamma}$ is quasi-projective? 

So for the second question, the thing that I have in mind would be to 1) construct some complex analytic immersion $\pi:\mathcal{E}_{\Gamma}\rightarrow Z$, where $Z$ is
a quasi-projective surface and 2) performing a sequence of blow-ups on $Z$ I would try to construct an embedding.