Actually the definition of $\gcd(a,b)$, valid in any P.I.D., is that it is a generator of the ideal $(a,b)$. In $\mathbf Z$, there are two generators, but there is a canonical way to choose one: it is to take the positive generator. In $F[X]$ ($F$ a field), we usually choose the monic generator.
In other P.I.D.s, there is usually no canonical way, as the g.c.d. is defined within a unit factor. For instance, in ring of Gaussian integers $\mathbf Z[i]$, the units are $\;\{1,-1,i,-i\}$ and there is no specific reason to choose one particular g.c.d.
The dual characterization of the l.c.m. of $a$ and $b$ is that it is a generator of the ideal $\;(a)\cap (b)$. In $\mathbf Z$, we likewise choose the positive generator.