I don't know any reference where such a presentation is written down for any Artin group. But:

• You can find here a presentation for the pure Artin group of type B: http://arxiv.org/abs/math/0408035 Proposition 1.1 (by setting $N=2$ is the formulaes)
• For all the infinite families, the corresponding pure braid groups are iterated semi-direct products of free groups. (For all the families but the $D_n$ one, it follows from the fact that the corresponding hyperplane arrangements are of fiber type, hence these are even almost-direct product). It should leads quite easily to a nice presentation of these groups.

I don't know any reference where such a presentation is written down for any Artin group. But:

• You can find In this paper of Enriquez a presentation for the pure Artin group of type B: http://arxiv.org/abs/math/0408035 Proposition 1.1 (by setting $N=2$ is the formulaes)
• For all the infinite families, the corresponding pure braid groups are iterated semi-direct products of free groups. (For all the families but the $D_n$ one, it follows from the fact that the corresponding hyperplane arrangements are of fiber type, hence these are even almost-direct product). It should leads quite easily to a nice presentation of these groups.

Edit: You may also be interested by this paper of Crips and Paris: http://arxiv.org/abs/math/0210438. Recall that $W_{B_n}=(\mathbb{Z}/2\mathbb{Z})^n \rtimes S_n$ and that $W_{D_n}=(\mathbb{Z}/2\mathbb{Z})^{n-1}\rtimes S_n$. It is proved in this paper that $B_{B_n}=F_n \rtimes B_n$ and that $B_{D_n}=F_{n-1}\rtimes B_n$ where $B_n$ is the braid group of type $A$ and $F_n$ is a free group, and that the canonical projection from the braid group to the Coxeter group is compatible with these decomposition (in the sense that in both cases it restricts to the obvious projections $B_n \rightarrow S_n$ and $F_k \rightarrow (\mathbb{Z}/2\mathbb{Z})^k$).